Starting phenix.real_space_refine on Tue Feb 11 19:14:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl8_19334/02_2025/8rl8_19334_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl8_19334/02_2025/8rl8_19334.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/8rl8_19334/02_2025/8rl8_19334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl8_19334/02_2025/8rl8_19334.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl8_19334/02_2025/8rl8_19334_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl8_19334/02_2025/8rl8_19334_trim.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= 0.011 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: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2116 2.51 5 N 526 2.21 5 O 558 1.98 5 H 3252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 6469 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6445 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.11, per 1000 atoms: 0.79 Number of scatterers: 6469 At special positions: 0 Unit cell: (82.071, 72.952, 67.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 558 8.00 N 526 7.00 C 2116 6.00 H 3252 1.00 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: 1.79 Conformation dependent library (CDL) restraints added in 611.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 94.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 100 through 125 removed outlier: 4.716A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.686A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 186 removed outlier: 3.718A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.691A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 257 removed outlier: 4.321A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.207A pdb=" N VAL A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 392 removed outlier: 3.654A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 391 " --> pdb=" O TRP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.859A pdb=" N LEU A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.731A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 525 removed outlier: 4.132A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 283 hydrogen bonds defined for protein. 840 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: 2.49 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3244 1.03 - 1.23: 8 1.23 - 1.42: 1389 1.42 - 1.61: 1876 1.61 - 1.81: 26 Bond restraints: 6543 Sorted by residual: bond pdb=" C3' LMT A 601 " pdb=" O3' LMT A 601 " ideal model delta sigma weight residual 1.404 1.363 0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C6' LMT A 601 " pdb=" O6' LMT A 601 " ideal model delta sigma weight residual 1.407 1.369 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C4 LMT A 601 " pdb=" C5 LMT A 601 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C8 LMT A 601 " pdb=" C9 LMT A 601 " ideal model delta sigma weight residual 1.531 1.495 0.036 2.00e-02 2.50e+03 3.18e+00 ... (remaining 6538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11670 1.81 - 3.62: 99 3.62 - 5.43: 14 5.43 - 7.25: 2 7.25 - 9.06: 3 Bond angle restraints: 11788 Sorted by residual: angle pdb=" N TRP A 178 " pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " ideal model delta sigma weight residual 110.30 115.08 -4.78 1.54e+00 4.22e-01 9.65e+00 angle pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " pdb=" C4 LMT A 601 " ideal model delta sigma weight residual 117.09 108.03 9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 115.63 5.05 1.70e+00 3.46e-01 8.84e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.06 -5.46 1.90e+00 2.77e-01 8.26e+00 angle pdb=" C10 LMT A 601 " pdb=" C9 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 116.03 107.82 8.21 3.00e+00 1.11e-01 7.50e+00 ... (remaining 11783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 2772 16.41 - 32.82: 220 32.82 - 49.22: 46 49.22 - 65.63: 61 65.63 - 82.04: 2 Dihedral angle restraints: 3101 sinusoidal: 1638 harmonic: 1463 Sorted by residual: dihedral pdb=" CA ARG A 342 " pdb=" CB ARG A 342 " pdb=" CG ARG A 342 " pdb=" CD ARG A 342 " ideal model delta sinusoidal sigma weight residual -60.00 -103.91 43.91 3 1.50e+01 4.44e-03 7.90e+00 dihedral pdb=" CB MET A 230 " pdb=" CG MET A 230 " pdb=" SD MET A 230 " pdb=" CE MET A 230 " ideal model delta sinusoidal sigma weight residual 60.00 102.50 -42.50 3 1.50e+01 4.44e-03 7.63e+00 dihedral pdb=" CA LYS A 391 " pdb=" CB LYS A 391 " pdb=" CG LYS A 391 " pdb=" CD LYS A 391 " ideal model delta sinusoidal sigma weight residual -180.00 -138.28 -41.72 3 1.50e+01 4.44e-03 7.47e+00 ... (remaining 3098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 418 0.039 - 0.079: 87 0.079 - 0.118: 22 0.118 - 0.158: 2 0.158 - 0.197: 2 Chirality restraints: 531 Sorted by residual: chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.75 0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" C5' LMT A 601 " pdb=" C4' LMT A 601 " pdb=" C6' LMT A 601 " pdb=" O5' LMT A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.32 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 528 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.019 2.00e-02 2.50e+03 1.25e-02 6.25e+00 pdb=" CG TRP A 178 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 178 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 178 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 178 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 509 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 188 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 189 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.025 5.00e-02 4.00e+02 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 660 2.24 - 2.83: 14649 2.83 - 3.42: 18019 3.42 - 4.01: 23277 4.01 - 4.60: 36325 Nonbonded interactions: 92930 Sorted by model distance: nonbonded pdb=" O PHE A 183 " pdb=" HG SER A 186 " model vdw 1.652 2.450 nonbonded pdb=" HH TYR A 315 " pdb=" O ALA A 459 " model vdw 1.711 2.450 nonbonded pdb=" O SER A 483 " pdb=" HG SER A 500 " model vdw 1.712 2.450 nonbonded pdb=" HG SER A 150 " pdb=" O GLY A 201 " model vdw 1.768 2.450 nonbonded pdb="HE22 GLN A 344 " pdb=" OD1 ASP A 362 " model vdw 1.829 2.450 ... (remaining 92925 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: 2.800 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.980 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 : 0.003 0.041 3291 Z= 0.219 Angle : 0.590 9.058 4471 Z= 0.305 Chirality : 0.037 0.197 531 Planarity : 0.004 0.046 544 Dihedral : 12.359 82.040 1143 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.43 (0.41), residues: 415 helix: 1.31 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.13 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.017 0.001 PHE A 526 TYR 0.014 0.001 TYR A 449 ARG 0.004 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8404 (t80) cc_final: 0.8001 (t80) REVERT: A 227 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6942 (ttm-80) REVERT: A 366 PHE cc_start: 0.7826 (t80) cc_final: 0.7436 (t80) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 1.7337 time to fit residues: 133.6142 Evaluate side-chains 70 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 393 GLN A 536 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145192 restraints weight = 12954.782| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.68 r_work: 0.3906 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3291 Z= 0.442 Angle : 0.671 7.859 4471 Z= 0.363 Chirality : 0.042 0.150 531 Planarity : 0.006 0.055 544 Dihedral : 5.141 40.995 488 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 11.14 % Favored : 86.45 % 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: 1.35 (0.40), residues: 415 helix: 1.21 (0.26), residues: 364 sheet: None (None), residues: 0 loop : -0.98 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 178 HIS 0.007 0.002 HIS A 341 PHE 0.022 0.003 PHE A 526 TYR 0.012 0.002 TYR A 503 ARG 0.003 0.001 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7189 (ttm-80) REVERT: A 389 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.3605 (mtp180) REVERT: A 390 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7033 (tt) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 1.9270 time to fit residues: 145.8642 Evaluate side-chains 77 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 311 ARG Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 448 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.160962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149507 restraints weight = 13082.994| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.69 r_work: 0.3953 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3291 Z= 0.184 Angle : 0.520 5.321 4471 Z= 0.274 Chirality : 0.036 0.131 531 Planarity : 0.004 0.053 544 Dihedral : 3.788 21.322 485 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.71 % Allowed : 12.95 % Favored : 84.34 % 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: 2.22 (0.41), residues: 415 helix: 1.80 (0.27), residues: 363 sheet: None (None), residues: 0 loop : -0.75 (0.86), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 410 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7280 (ttm-80) REVERT: A 242 SER cc_start: 0.8270 (p) cc_final: 0.8040 (m) REVERT: A 390 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7011 (tt) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 1.9091 time to fit residues: 140.5263 Evaluate side-chains 72 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 overall best weight: 0.2758 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.160110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148611 restraints weight = 13222.777| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.69 r_work: 0.3942 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3291 Z= 0.216 Angle : 0.524 5.985 4471 Z= 0.277 Chirality : 0.036 0.130 531 Planarity : 0.004 0.051 544 Dihedral : 3.742 22.660 485 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.33 % 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: 2.29 (0.41), residues: 415 helix: 1.86 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.12 (0.85), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.014 0.001 PHE A 410 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7300 (ttm-80) REVERT: A 242 SER cc_start: 0.8307 (p) cc_final: 0.8073 (m) REVERT: A 390 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (tt) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 1.8643 time to fit residues: 137.4203 Evaluate side-chains 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.158862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147233 restraints weight = 13056.591| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.72 r_work: 0.3929 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3291 Z= 0.258 Angle : 0.529 5.478 4471 Z= 0.285 Chirality : 0.037 0.132 531 Planarity : 0.005 0.051 544 Dihedral : 3.831 26.803 485 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.31 % Allowed : 17.17 % Favored : 79.52 % 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: 2.25 (0.41), residues: 415 helix: 1.80 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.02 (0.90), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.016 0.002 PHE A 410 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7294 (ttm-80) REVERT: A 242 SER cc_start: 0.8329 (p) cc_final: 0.8119 (m) REVERT: A 261 TRP cc_start: 0.7462 (m100) cc_final: 0.6450 (m100) REVERT: A 390 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7066 (tt) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 1.9263 time to fit residues: 151.8949 Evaluate side-chains 80 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.155789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.144222 restraints weight = 13053.751| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.69 r_work: 0.3891 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3291 Z= 0.379 Angle : 0.589 5.573 4471 Z= 0.321 Chirality : 0.039 0.142 531 Planarity : 0.005 0.050 544 Dihedral : 4.217 34.474 485 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.92 % Allowed : 18.98 % Favored : 77.11 % 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: 1.92 (0.41), residues: 415 helix: 1.57 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -0.95 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.021 0.002 PHE A 410 TYR 0.012 0.002 TYR A 339 ARG 0.003 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7388 (ttm-80) REVERT: A 242 SER cc_start: 0.8280 (p) cc_final: 0.8079 (m) REVERT: A 390 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7096 (tt) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 1.8753 time to fit residues: 146.0722 Evaluate side-chains 80 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.157134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145421 restraints weight = 13339.248| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.72 r_work: 0.3905 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3291 Z= 0.275 Angle : 0.540 5.500 4471 Z= 0.290 Chirality : 0.037 0.135 531 Planarity : 0.005 0.050 544 Dihedral : 4.077 32.102 485 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.52 % Allowed : 18.07 % Favored : 77.41 % 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: 2.16 (0.41), residues: 415 helix: 1.75 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.93 (0.90), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 PHE 0.018 0.002 PHE A 410 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7413 (ttm-80) REVERT: A 242 SER cc_start: 0.8267 (p) cc_final: 0.8055 (m) REVERT: A 390 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7106 (tt) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 1.8875 time to fit residues: 146.9802 Evaluate side-chains 80 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145171 restraints weight = 13348.372| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.77 r_work: 0.3901 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3291 Z= 0.281 Angle : 0.543 5.483 4471 Z= 0.293 Chirality : 0.037 0.137 531 Planarity : 0.005 0.050 544 Dihedral : 4.085 32.013 485 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.22 % Allowed : 18.98 % Favored : 76.81 % 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: 2.19 (0.42), residues: 415 helix: 1.77 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.86 (0.94), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.018 0.002 PHE A 410 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7410 (ttm-80) REVERT: A 242 SER cc_start: 0.8295 (p) cc_final: 0.8088 (m) REVERT: A 389 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5838 (mtp180) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 1.8348 time to fit residues: 141.3626 Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.157662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145755 restraints weight = 13434.902| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.77 r_work: 0.3907 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3291 Z= 0.257 Angle : 0.535 5.481 4471 Z= 0.287 Chirality : 0.037 0.135 531 Planarity : 0.004 0.050 544 Dihedral : 4.041 31.090 485 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.92 % Allowed : 18.98 % Favored : 77.11 % 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 (0.42), residues: 415 helix: 1.83 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.82 (0.94), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.016 0.002 PHE A 410 TYR 0.013 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: A 242 SER cc_start: 0.8295 (p) cc_final: 0.8086 (m) REVERT: A 261 TRP cc_start: 0.7441 (m100) cc_final: 0.6468 (m100) REVERT: A 390 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7058 (tt) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 1.8966 time to fit residues: 143.5761 Evaluate side-chains 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 39 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.160486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148450 restraints weight = 13426.006| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.82 r_work: 0.3939 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3291 Z= 0.168 Angle : 0.502 6.105 4471 Z= 0.264 Chirality : 0.036 0.122 531 Planarity : 0.004 0.051 544 Dihedral : 3.768 25.307 485 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.41 % Allowed : 20.18 % Favored : 77.41 % 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: 2.68 (0.42), residues: 415 helix: 2.10 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.76 (0.96), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 PHE 0.013 0.001 PHE A 410 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7378 (ttm-80) REVERT: A 242 SER cc_start: 0.8125 (p) cc_final: 0.7903 (m) REVERT: A 261 TRP cc_start: 0.7380 (m100) cc_final: 0.6420 (m100) REVERT: A 390 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7050 (tt) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 1.8970 time to fit residues: 143.7206 Evaluate side-chains 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145821 restraints weight = 13566.438| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.82 r_work: 0.3907 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3291 Z= 0.267 Angle : 0.539 5.472 4471 Z= 0.289 Chirality : 0.037 0.136 531 Planarity : 0.005 0.050 544 Dihedral : 3.932 29.260 485 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.01 % Allowed : 19.88 % Favored : 77.11 % 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: 2.48 (0.42), residues: 415 helix: 1.97 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.84 (0.94), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 PHE 0.017 0.002 PHE A 410 TYR 0.013 0.001 TYR A 339 ARG 0.004 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5832.58 seconds wall clock time: 103 minutes 36.68 seconds (6216.68 seconds total)