Starting phenix.real_space_refine on Fri Aug 22 17:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl8_19334/08_2025/8rl8_19334_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl8_19334/08_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_19334/08_2025/8rl8_19334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl8_19334/08_2025/8rl8_19334.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl8_19334/08_2025/8rl8_19334_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl8_19334/08_2025/8rl8_19334_trim.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLU:plan': 1} 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: 1.15, per 1000 atoms: 0.18 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: 0.51 Conformation dependent library (CDL) restraints added in 190.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.10 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: 1.14 Time building geometry restraints manager: 0.69 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: 5.420 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: 0.040 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- 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= 0.167 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 : 7.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 227 TYR 0.014 0.001 TYR A 449 PHE 0.017 0.001 PHE A 526 TRP 0.042 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3291) covalent geometry : angle 0.59006 ( 4471) hydrogen bonds : bond 0.11034 ( 283) hydrogen bonds : angle 5.06581 ( 840) *********************** 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 : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.7158 time to fit residues: 55.0826 Evaluate side-chains 69 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 37 optimal weight: 0.0980 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 190 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 = 0.4196 r_free = 0.4196 target = 0.164618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.153102 restraints weight = 13238.742| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.71 r_work: 0.3999 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1650 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= 0.139 Angle : 0.533 5.258 4471 Z= 0.278 Chirality : 0.036 0.122 531 Planarity : 0.005 0.050 544 Dihedral : 4.753 44.080 488 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 9.34 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.42), residues: 415 helix: 1.78 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.55 (0.92), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.008 0.001 TYR A 116 PHE 0.010 0.001 PHE A 526 TRP 0.033 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3291) covalent geometry : angle 0.53291 ( 4471) hydrogen bonds : bond 0.05139 ( 283) hydrogen bonds : angle 4.33561 ( 840) *********************** 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 73 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8385 (t80) cc_final: 0.8100 (t80) REVERT: A 227 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7181 (ttm-80) REVERT: A 390 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6983 (tt) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.8042 time to fit residues: 55.8174 Evaluate side-chains 68 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 311 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.0770 chunk 41 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.158129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146555 restraints weight = 13041.550| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.71 r_work: 0.3922 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3291 Z= 0.239 Angle : 0.591 6.437 4471 Z= 0.318 Chirality : 0.038 0.141 531 Planarity : 0.005 0.051 544 Dihedral : 4.016 26.680 485 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 12.65 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.41), residues: 415 helix: 1.61 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -0.78 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.010 0.002 TYR A 339 PHE 0.020 0.002 PHE A 526 TRP 0.041 0.003 TRP A 178 HIS 0.007 0.002 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 3291) covalent geometry : angle 0.59137 ( 4471) hydrogen bonds : bond 0.06304 ( 283) hydrogen bonds : angle 4.55624 ( 840) *********************** 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 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8513 (t80) cc_final: 0.8166 (t80) REVERT: A 227 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.7307 (ttm-80) REVERT: A 242 SER cc_start: 0.8311 (p) cc_final: 0.8087 (m) REVERT: A 390 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7053 (tt) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.8035 time to fit residues: 59.7994 Evaluate side-chains 74 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.156270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144820 restraints weight = 13218.093| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.69 r_work: 0.3899 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3124 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= 0.268 Angle : 0.609 6.708 4471 Z= 0.326 Chirality : 0.039 0.142 531 Planarity : 0.005 0.051 544 Dihedral : 4.161 30.578 485 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.01 % Allowed : 15.06 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.41), residues: 415 helix: 1.48 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.19 (0.85), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.011 0.002 TYR A 339 PHE 0.018 0.002 PHE A 526 TRP 0.038 0.003 TRP A 178 HIS 0.005 0.002 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 3291) covalent geometry : angle 0.60855 ( 4471) hydrogen bonds : bond 0.06430 ( 283) hydrogen bonds : angle 4.63528 ( 840) *********************** 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 84 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8473 (t80) cc_final: 0.8096 (t80) REVERT: A 227 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7340 (ttm-80) REVERT: A 242 SER cc_start: 0.8284 (p) cc_final: 0.8068 (m) REVERT: A 390 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7073 (tt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.7414 time to fit residues: 59.2109 Evaluate side-chains 81 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 127 LEU 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 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 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 41 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.157681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145922 restraints weight = 13522.565| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.78 r_work: 0.3888 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3288 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= 0.196 Angle : 0.545 5.602 4471 Z= 0.293 Chirality : 0.037 0.133 531 Planarity : 0.005 0.050 544 Dihedral : 4.039 30.827 485 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.31 % Allowed : 18.98 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.41), residues: 415 helix: 1.65 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.02 (0.88), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.012 0.001 TYR A 339 PHE 0.012 0.002 PHE A 526 TRP 0.037 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3291) covalent geometry : angle 0.54475 ( 4471) hydrogen bonds : bond 0.05846 ( 283) hydrogen bonds : angle 4.48939 ( 840) *********************** 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 85 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7582 (ttp-170) cc_final: 0.7359 (ttm-80) REVERT: A 242 SER cc_start: 0.8245 (p) cc_final: 0.8020 (m) REVERT: A 390 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7082 (tt) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.7759 time to fit residues: 62.7771 Evaluate side-chains 82 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 127 LEU 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 390 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.0670 chunk 4 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.158706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146992 restraints weight = 13403.094| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.76 r_work: 0.3903 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3291 Z= 0.167 Angle : 0.526 5.429 4471 Z= 0.281 Chirality : 0.036 0.131 531 Planarity : 0.004 0.050 544 Dihedral : 3.919 28.628 485 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.92 % Allowed : 18.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.42), residues: 415 helix: 1.85 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.96 (0.92), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.014 0.001 TYR A 339 PHE 0.026 0.002 PHE A 193 TRP 0.035 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3291) covalent geometry : angle 0.52641 ( 4471) hydrogen bonds : bond 0.05493 ( 283) hydrogen bonds : angle 4.35366 ( 840) *********************** 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 85 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7301 (ttm-80) REVERT: A 242 SER cc_start: 0.8256 (p) cc_final: 0.8026 (m) REVERT: A 390 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7027 (tt) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.9780 time to fit residues: 76.9719 Evaluate side-chains 80 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 2 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.158941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147012 restraints weight = 13320.257| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.81 r_work: 0.3901 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3431 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= 0.161 Angle : 0.529 5.420 4471 Z= 0.279 Chirality : 0.036 0.132 531 Planarity : 0.004 0.050 544 Dihedral : 3.869 28.203 485 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.52 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.42), residues: 415 helix: 1.90 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.95 (0.93), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.013 0.001 TYR A 339 PHE 0.018 0.001 PHE A 193 TRP 0.035 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3291) covalent geometry : angle 0.52857 ( 4471) hydrogen bonds : bond 0.05380 ( 283) hydrogen bonds : angle 4.31525 ( 840) *********************** 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 87 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7345 (ttm-80) REVERT: A 242 SER cc_start: 0.8274 (p) cc_final: 0.8046 (m) REVERT: A 261 TRP cc_start: 0.7441 (m100) cc_final: 0.6485 (m100) REVERT: A 390 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7037 (tt) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 0.9478 time to fit residues: 76.6108 Evaluate side-chains 78 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.156583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.145054 restraints weight = 13410.135| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.75 r_work: 0.3880 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3291 Z= 0.243 Angle : 0.576 5.627 4471 Z= 0.311 Chirality : 0.039 0.141 531 Planarity : 0.005 0.049 544 Dihedral : 4.197 34.044 485 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.61 % Allowed : 18.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.42), residues: 415 helix: 1.68 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.86 (0.95), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 264 TYR 0.015 0.002 TYR A 339 PHE 0.017 0.002 PHE A 193 TRP 0.039 0.002 TRP A 178 HIS 0.006 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 3291) covalent geometry : angle 0.57635 ( 4471) hydrogen bonds : bond 0.06107 ( 283) hydrogen bonds : angle 4.51911 ( 840) *********************** 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: 12 poor density : 71 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7402 (ttm-80) REVERT: A 242 SER cc_start: 0.8281 (p) cc_final: 0.8072 (m) REVERT: A 261 TRP cc_start: 0.7482 (m100) cc_final: 0.6634 (m100) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 1.0362 time to fit residues: 80.3770 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 : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 427 ILE 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 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 27 optimal weight: 0.0970 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.159514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147737 restraints weight = 13425.047| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.81 r_work: 0.3912 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3291 Z= 0.147 Angle : 0.518 5.482 4471 Z= 0.274 Chirality : 0.036 0.126 531 Planarity : 0.004 0.050 544 Dihedral : 3.893 28.050 485 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.71 % Allowed : 19.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.42), residues: 415 helix: 1.98 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.76 (0.98), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.014 0.001 TYR A 339 PHE 0.014 0.001 PHE A 193 TRP 0.035 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3291) covalent geometry : angle 0.51821 ( 4471) hydrogen bonds : bond 0.05208 ( 283) hydrogen bonds : angle 4.28255 ( 840) *********************** 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 79 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7357 (ttm-80) REVERT: A 242 SER cc_start: 0.8261 (p) cc_final: 0.8037 (m) REVERT: A 261 TRP cc_start: 0.7392 (m100) cc_final: 0.6464 (m100) REVERT: A 390 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7034 (tt) outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.9682 time to fit residues: 75.1723 Evaluate side-chains 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 40 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 overall best weight: 0.2358 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.159560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.147845 restraints weight = 13233.467| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.75 r_work: 0.3922 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3665 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= 0.152 Angle : 0.527 5.605 4471 Z= 0.278 Chirality : 0.036 0.131 531 Planarity : 0.004 0.049 544 Dihedral : 3.840 27.477 485 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 21.39 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.42), residues: 415 helix: 2.04 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.82 (0.98), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.012 0.001 TYR A 339 PHE 0.013 0.001 PHE A 193 TRP 0.035 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3291) covalent geometry : angle 0.52714 ( 4471) hydrogen bonds : bond 0.05232 ( 283) hydrogen bonds : angle 4.23954 ( 840) ********************** 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 75 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 SER cc_start: 0.8275 (p) cc_final: 0.8050 (m) REVERT: A 261 TRP cc_start: 0.7380 (m100) cc_final: 0.6446 (m100) REVERT: A 390 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7051 (tt) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.8358 time to fit residues: 62.4422 Evaluate side-chains 73 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 5 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.160451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148587 restraints weight = 13335.968| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.80 r_work: 0.3940 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3291 Z= 0.133 Angle : 0.506 5.400 4471 Z= 0.266 Chirality : 0.036 0.127 531 Planarity : 0.004 0.049 544 Dihedral : 3.751 25.494 485 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.41 % Allowed : 21.39 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.42), residues: 415 helix: 2.18 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.63 (0.97), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 456 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE A 193 TRP 0.033 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3291) covalent geometry : angle 0.50553 ( 4471) hydrogen bonds : bond 0.04955 ( 283) hydrogen bonds : angle 4.16314 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.77 seconds wall clock time: 47 minutes 44.23 seconds (2864.23 seconds total)