Starting phenix.real_space_refine on Thu Jul 2 00:26:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmm_66097/07_2026/9wmm_66097.map" } resolution = 2.8 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= -0.003 sd= 0.119 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3062 2.51 5 N 657 2.21 5 O 734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4489 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 224 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 3, 'Y01': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 2 Time building chain proxies: 1.11, per 1000 atoms: 0.25 Number of scatterers: 4489 At special positions: 0 Unit cell: (82.159, 73.623, 73.623, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 734 8.00 N 657 7.00 C 3062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.40 Conformation dependent library (CDL) restraints added in 225.6 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 78.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.538A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.547A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.601A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.994A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.190A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.517A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.242A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.824A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.563A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.792A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.643A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 290 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 638 1.31 - 1.44: 1322 1.44 - 1.56: 2625 1.56 - 1.69: 2 1.69 - 1.81: 54 Bond restraints: 4641 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.28e-02 6.10e+03 1.66e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.505 -0.049 1.41e-02 5.03e+03 1.19e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" N VAL A 592 " pdb=" CA VAL A 592 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.64e+00 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.05e-02 9.07e+03 9.63e+00 ... (remaining 4636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5946 1.69 - 3.37: 335 3.37 - 5.06: 69 5.06 - 6.75: 10 6.75 - 8.43: 5 Bond angle restraints: 6365 Sorted by residual: angle pdb=" N ARG A 321 " pdb=" CA ARG A 321 " pdb=" C ARG A 321 " ideal model delta sigma weight residual 111.11 105.41 5.70 1.20e+00 6.94e-01 2.26e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.30 4.52 1.05e+00 9.07e-01 1.85e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.63 4.19 1.05e+00 9.07e-01 1.59e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.29 4.13 1.06e+00 8.90e-01 1.51e+01 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 111.71 107.36 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 6360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 2702 24.49 - 48.98: 222 48.98 - 73.47: 32 73.47 - 97.96: 13 97.96 - 122.45: 6 Dihedral angle restraints: 2975 sinusoidal: 1425 harmonic: 1550 Sorted by residual: dihedral pdb=" C10 CLR A 703 " pdb=" C1 CLR A 703 " pdb=" C2 CLR A 703 " pdb=" C3 CLR A 703 " ideal model delta sinusoidal sigma weight residual -56.83 65.62 -122.45 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C10 CLR A 709 " pdb=" C1 CLR A 709 " pdb=" C2 CLR A 709 " pdb=" C3 CLR A 709 " ideal model delta sinusoidal sigma weight residual -56.83 65.36 -122.19 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C10 CLR A 706 " pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " ideal model delta sinusoidal sigma weight residual -56.83 63.18 -120.01 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 2972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 614 0.062 - 0.125: 96 0.125 - 0.187: 16 0.187 - 0.249: 2 0.249 - 0.311: 2 Chirality restraints: 730 Sorted by residual: chirality pdb=" CBE Y01 A 704 " pdb=" CAP Y01 A 704 " pdb=" CBB Y01 A 704 " pdb=" CBI Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.57 2.26 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C8 CLR A 703 " pdb=" C14 CLR A 703 " pdb=" C7 CLR A 703 " pdb=" C9 CLR A 703 " both_signs ideal model delta sigma weight residual False 2.69 2.39 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN A 134 " pdb=" N ASN A 134 " pdb=" C ASN A 134 " pdb=" CB ASN A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 727 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 321 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 321 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 322 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO A 523 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C LEU A 471 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.015 2.00e-02 2.50e+03 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1560 2.86 - 3.37: 4544 3.37 - 3.88: 8039 3.88 - 4.39: 9746 4.39 - 4.90: 15810 Nonbonded interactions: 39699 Sorted by model distance: nonbonded pdb=" O LEU A 144 " pdb=" OG SER A 147 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.354 3.210 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.383 3.040 nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 2.424 3.210 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.433 3.040 ... (remaining 39694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.270 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4642 Z= 0.337 Angle : 0.892 8.434 6367 Z= 0.536 Chirality : 0.050 0.311 730 Planarity : 0.006 0.065 734 Dihedral : 18.537 122.446 1990 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % 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 are not related in a simple way. whole: 0.34 (0.35), residues: 536 helix: 0.93 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.012 0.001 PHE A 245 TRP 0.027 0.002 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.34 ( 4641) covalent geometry : angle 0.89172 / 0.54 ( 6365) SS BOND : bond 0.00289 / 0.15 ( 1) SS BOND : angle 0.51790 / 0.30 ( 2) hydrogen bonds : bond 0.12558 / 8.23 ( 290) hydrogen bonds : angle 5.90014 / 4.05 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.157 Fit side-chains REVERT: A 155 GLU cc_start: 0.8696 (tt0) cc_final: 0.8436 (tt0) REVERT: A 358 GLN cc_start: 0.8044 (pt0) cc_final: 0.7754 (pt0) REVERT: A 398 ASP cc_start: 0.7105 (m-30) cc_final: 0.6868 (m-30) REVERT: A 434 MET cc_start: 0.8645 (mtt) cc_final: 0.8394 (mtt) REVERT: A 489 MET cc_start: 0.8935 (ttp) cc_final: 0.8527 (mtm) REVERT: A 554 MET cc_start: 0.8627 (mtt) cc_final: 0.8405 (mtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4692 time to fit residues: 52.7800 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132071 restraints weight = 5146.884| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.49 r_work: 0.3493 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4642 Z= 0.136 Angle : 0.651 9.290 6367 Z= 0.297 Chirality : 0.040 0.231 730 Planarity : 0.005 0.047 734 Dihedral : 10.862 63.112 1063 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.19 % Allowed : 18.32 % Favored : 77.48 % 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 are not related in a simple way. whole: 1.50 (0.36), residues: 536 helix: 1.79 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.97 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 420 TYR 0.016 0.001 TYR A 320 PHE 0.015 0.001 PHE A 245 TRP 0.014 0.001 TRP A 215 HIS 0.001 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 4641) covalent geometry : angle 0.65071 / 0.30 ( 6365) SS BOND : bond 0.00177 / 0.09 ( 1) SS BOND : angle 0.18544 / 0.10 ( 2) hydrogen bonds : bond 0.04613 / 3.02 ( 290) hydrogen bonds : angle 4.63754 / 3.22 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.095 Fit side-chains REVERT: A 40 TRP cc_start: 0.6567 (t60) cc_final: 0.6194 (t-100) REVERT: A 43 LYS cc_start: 0.8008 (mptt) cc_final: 0.7650 (mptt) REVERT: A 133 TYR cc_start: 0.7458 (m-10) cc_final: 0.7045 (m-80) REVERT: A 309 PHE cc_start: 0.4952 (t80) cc_final: 0.3855 (t80) REVERT: A 317 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: A 339 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7191 (t80) REVERT: A 489 MET cc_start: 0.9002 (ttp) cc_final: 0.8493 (mtm) REVERT: A 525 GLU cc_start: 0.8151 (pt0) cc_final: 0.7667 (pm20) REVERT: A 554 MET cc_start: 0.8549 (mtt) cc_final: 0.8312 (mtt) outliers start: 19 outliers final: 4 residues processed: 95 average time/residue: 0.3883 time to fit residues: 38.3815 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 578 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130334 restraints weight = 5225.022| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.50 r_work: 0.3471 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4642 Z= 0.132 Angle : 0.577 5.930 6367 Z= 0.268 Chirality : 0.039 0.243 730 Planarity : 0.004 0.037 734 Dihedral : 9.930 59.558 1063 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.21 % Allowed : 19.43 % Favored : 78.37 % 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 are not related in a simple way. whole: 1.78 (0.36), residues: 536 helix: 1.99 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.83 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 245 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4641) covalent geometry : angle 0.57722 / 0.27 ( 6365) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 0.17772 / 0.10 ( 2) hydrogen bonds : bond 0.04421 / 2.89 ( 290) hydrogen bonds : angle 4.48073 / 3.12 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.111 Fit side-chains REVERT: A 40 TRP cc_start: 0.6574 (t60) cc_final: 0.6151 (t-100) REVERT: A 43 LYS cc_start: 0.8175 (mptt) cc_final: 0.7745 (mptt) REVERT: A 53 TYR cc_start: 0.7070 (t80) cc_final: 0.6446 (t80) REVERT: A 133 TYR cc_start: 0.7231 (m-10) cc_final: 0.6718 (m-80) REVERT: A 156 HIS cc_start: 0.7976 (m90) cc_final: 0.7733 (m170) REVERT: A 278 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: A 309 PHE cc_start: 0.4913 (t80) cc_final: 0.3949 (t80) REVERT: A 489 MET cc_start: 0.8979 (ttp) cc_final: 0.8572 (mtm) REVERT: A 525 GLU cc_start: 0.8073 (pt0) cc_final: 0.7604 (pm20) REVERT: A 554 MET cc_start: 0.8574 (mtt) cc_final: 0.8333 (mtt) outliers start: 10 outliers final: 3 residues processed: 90 average time/residue: 0.3835 time to fit residues: 36.1212 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126216 restraints weight = 5206.079| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.38 r_work: 0.3398 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4642 Z= 0.145 Angle : 0.564 5.987 6367 Z= 0.265 Chirality : 0.039 0.249 730 Planarity : 0.004 0.034 734 Dihedral : 9.918 57.814 1063 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.87 % Allowed : 19.65 % Favored : 77.48 % 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 are not related in a simple way. whole: 1.81 (0.36), residues: 536 helix: 1.97 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 321 TYR 0.017 0.001 TYR A 132 PHE 0.011 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4641) covalent geometry : angle 0.56399 / 0.27 ( 6365) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 0.12457 / 0.07 ( 2) hydrogen bonds : bond 0.04520 / 2.94 ( 290) hydrogen bonds : angle 4.49500 / 3.15 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.157 Fit side-chains REVERT: A 40 TRP cc_start: 0.6556 (t60) cc_final: 0.6180 (t-100) REVERT: A 43 LYS cc_start: 0.8347 (mptt) cc_final: 0.7888 (mptt) REVERT: A 53 TYR cc_start: 0.7376 (t80) cc_final: 0.7098 (t80) REVERT: A 133 TYR cc_start: 0.7448 (m-10) cc_final: 0.6881 (m-80) REVERT: A 278 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: A 309 PHE cc_start: 0.4972 (t80) cc_final: 0.4074 (t80) REVERT: A 489 MET cc_start: 0.8965 (ttp) cc_final: 0.8586 (mtm) REVERT: A 525 GLU cc_start: 0.8065 (pt0) cc_final: 0.7672 (pm20) outliers start: 13 outliers final: 4 residues processed: 86 average time/residue: 0.3476 time to fit residues: 31.4037 Evaluate side-chains 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125439 restraints weight = 5215.880| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.40 r_work: 0.3382 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4642 Z= 0.148 Angle : 0.558 6.048 6367 Z= 0.263 Chirality : 0.039 0.273 730 Planarity : 0.004 0.035 734 Dihedral : 9.853 59.949 1063 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.65 % Allowed : 18.54 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.35), residues: 536 helix: 2.01 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.57 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 321 TYR 0.017 0.001 TYR A 132 PHE 0.009 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 4641) covalent geometry : angle 0.55796 / 0.26 ( 6365) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.21609 / 0.12 ( 2) hydrogen bonds : bond 0.04489 / 2.93 ( 290) hydrogen bonds : angle 4.45378 / 3.12 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.175 Fit side-chains REVERT: A 40 TRP cc_start: 0.6533 (t60) cc_final: 0.6204 (t-100) REVERT: A 43 LYS cc_start: 0.8488 (mptt) cc_final: 0.8072 (mptt) REVERT: A 133 TYR cc_start: 0.7679 (m-10) cc_final: 0.7088 (m-80) REVERT: A 278 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: A 309 PHE cc_start: 0.5016 (t80) cc_final: 0.4139 (t80) REVERT: A 489 MET cc_start: 0.9008 (ttp) cc_final: 0.8644 (mtm) REVERT: A 525 GLU cc_start: 0.8056 (pt0) cc_final: 0.7708 (pm20) REVERT: A 584 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7631 (tt0) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 0.3791 time to fit residues: 33.7955 Evaluate side-chains 77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 156 HIS A 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125432 restraints weight = 5228.979| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.41 r_work: 0.3386 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4642 Z= 0.146 Angle : 0.555 5.887 6367 Z= 0.262 Chirality : 0.039 0.269 730 Planarity : 0.004 0.035 734 Dihedral : 9.698 57.675 1063 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.77 % Allowed : 19.87 % Favored : 78.37 % 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 are not related in a simple way. whole: 1.90 (0.36), residues: 536 helix: 2.01 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.58 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.016 0.001 TYR A 132 PHE 0.010 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 4641) covalent geometry : angle 0.55556 / 0.26 ( 6365) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 0.20600 / 0.12 ( 2) hydrogen bonds : bond 0.04477 / 2.91 ( 290) hydrogen bonds : angle 4.46350 / 3.13 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.101 Fit side-chains REVERT: A 40 TRP cc_start: 0.6483 (t60) cc_final: 0.6128 (t-100) REVERT: A 43 LYS cc_start: 0.8422 (mptt) cc_final: 0.7979 (mptt) REVERT: A 133 TYR cc_start: 0.7600 (m-10) cc_final: 0.7055 (m-80) REVERT: A 278 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: A 280 HIS cc_start: 0.8067 (p-80) cc_final: 0.7804 (p90) REVERT: A 309 PHE cc_start: 0.5089 (t80) cc_final: 0.4195 (t80) REVERT: A 489 MET cc_start: 0.9027 (ttp) cc_final: 0.8689 (mtm) REVERT: A 525 GLU cc_start: 0.8040 (pt0) cc_final: 0.7676 (pm20) REVERT: A 584 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7588 (tt0) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.3394 time to fit residues: 29.8516 Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126226 restraints weight = 5216.245| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.40 r_work: 0.3399 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4642 Z= 0.135 Angle : 0.544 5.654 6367 Z= 0.256 Chirality : 0.038 0.264 730 Planarity : 0.004 0.035 734 Dihedral : 9.603 58.586 1063 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.55 % Allowed : 19.65 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.36), residues: 536 helix: 2.09 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.51 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.016 0.001 TYR A 132 PHE 0.008 0.001 PHE A 389 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 4641) covalent geometry : angle 0.54371 / 0.26 ( 6365) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.20940 / 0.12 ( 2) hydrogen bonds : bond 0.04354 / 2.83 ( 290) hydrogen bonds : angle 4.41540 / 3.10 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.107 Fit side-chains REVERT: A 40 TRP cc_start: 0.6477 (t60) cc_final: 0.6133 (t-100) REVERT: A 43 LYS cc_start: 0.8414 (mptt) cc_final: 0.7972 (mptt) REVERT: A 133 TYR cc_start: 0.7568 (m-10) cc_final: 0.7019 (m-80) REVERT: A 278 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: A 280 HIS cc_start: 0.8089 (p-80) cc_final: 0.7840 (p90) REVERT: A 309 PHE cc_start: 0.5076 (t80) cc_final: 0.4158 (t80) REVERT: A 456 TYR cc_start: 0.8682 (m-80) cc_final: 0.7730 (m-80) REVERT: A 460 PHE cc_start: 0.7548 (t80) cc_final: 0.6887 (m-80) REVERT: A 489 MET cc_start: 0.9023 (ttp) cc_final: 0.8694 (mtm) REVERT: A 525 GLU cc_start: 0.8043 (pt0) cc_final: 0.7689 (pm20) outliers start: 7 outliers final: 2 residues processed: 85 average time/residue: 0.3578 time to fit residues: 31.8230 Evaluate side-chains 77 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123129 restraints weight = 5203.813| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.40 r_work: 0.3358 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4642 Z= 0.180 Angle : 0.595 6.325 6367 Z= 0.280 Chirality : 0.041 0.297 730 Planarity : 0.004 0.034 734 Dihedral : 9.598 59.927 1063 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.32 % Allowed : 20.75 % Favored : 77.92 % 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 are not related in a simple way. whole: 1.83 (0.36), residues: 536 helix: 1.91 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.46 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 321 TYR 0.018 0.002 TYR A 132 PHE 0.013 0.001 PHE A 91 TRP 0.011 0.001 TRP A 225 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 4641) covalent geometry : angle 0.59503 / 0.28 ( 6365) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.42045 / 0.24 ( 2) hydrogen bonds : bond 0.04766 / 3.09 ( 290) hydrogen bonds : angle 4.55643 / 3.20 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.158 Fit side-chains REVERT: A 40 TRP cc_start: 0.6512 (t60) cc_final: 0.6121 (t-100) REVERT: A 43 LYS cc_start: 0.8455 (mptt) cc_final: 0.8004 (mptt) REVERT: A 133 TYR cc_start: 0.7678 (m-10) cc_final: 0.7098 (m-80) REVERT: A 278 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: A 280 HIS cc_start: 0.8185 (p-80) cc_final: 0.7919 (p90) REVERT: A 456 TYR cc_start: 0.8703 (m-80) cc_final: 0.7772 (m-80) REVERT: A 460 PHE cc_start: 0.7630 (t80) cc_final: 0.6933 (m-80) REVERT: A 489 MET cc_start: 0.9077 (ttp) cc_final: 0.8706 (mtm) REVERT: A 525 GLU cc_start: 0.8110 (pt0) cc_final: 0.7771 (pm20) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.4312 time to fit residues: 34.7484 Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 156 HIS A 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126045 restraints weight = 5174.173| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.42 r_work: 0.3392 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4642 Z= 0.133 Angle : 0.550 5.288 6367 Z= 0.262 Chirality : 0.039 0.254 730 Planarity : 0.004 0.037 734 Dihedral : 9.536 59.642 1063 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.10 % Allowed : 19.65 % Favored : 79.25 % 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 are not related in a simple way. whole: 1.98 (0.36), residues: 536 helix: 2.02 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.40 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.015 0.001 TYR A 132 PHE 0.010 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4641) covalent geometry : angle 0.54986 / 0.26 ( 6365) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.21233 / 0.11 ( 2) hydrogen bonds : bond 0.04370 / 2.84 ( 290) hydrogen bonds : angle 4.43014 / 3.10 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.158 Fit side-chains REVERT: A 40 TRP cc_start: 0.6554 (t60) cc_final: 0.6189 (t-100) REVERT: A 43 LYS cc_start: 0.8513 (mptt) cc_final: 0.8089 (mptt) REVERT: A 133 TYR cc_start: 0.7706 (m-10) cc_final: 0.7119 (m-80) REVERT: A 278 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: A 280 HIS cc_start: 0.8167 (p-80) cc_final: 0.7903 (p90) REVERT: A 309 PHE cc_start: 0.5211 (t80) cc_final: 0.4308 (t80) REVERT: A 456 TYR cc_start: 0.8660 (m-80) cc_final: 0.7724 (m-80) REVERT: A 489 MET cc_start: 0.9034 (ttp) cc_final: 0.8678 (mtm) REVERT: A 525 GLU cc_start: 0.8084 (pt0) cc_final: 0.7716 (pm20) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.4349 time to fit residues: 34.6318 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 156 HIS A 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126160 restraints weight = 5165.008| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.42 r_work: 0.3398 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4642 Z= 0.133 Angle : 0.550 5.357 6367 Z= 0.261 Chirality : 0.039 0.253 730 Planarity : 0.004 0.036 734 Dihedral : 9.389 59.024 1063 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.10 % Allowed : 19.65 % Favored : 79.25 % 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 are not related in a simple way. whole: 2.04 (0.36), residues: 536 helix: 2.06 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.40 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 530 TYR 0.015 0.001 TYR A 132 PHE 0.008 0.001 PHE A 389 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4641) covalent geometry : angle 0.55035 / 0.26 ( 6365) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.21013 / 0.11 ( 2) hydrogen bonds : bond 0.04343 / 2.82 ( 290) hydrogen bonds : angle 4.42600 / 3.10 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.166 Fit side-chains REVERT: A 40 TRP cc_start: 0.6514 (t60) cc_final: 0.6133 (t-100) REVERT: A 43 LYS cc_start: 0.8431 (mptt) cc_final: 0.7993 (mptt) REVERT: A 133 TYR cc_start: 0.7668 (m-10) cc_final: 0.7079 (m-80) REVERT: A 278 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: A 280 HIS cc_start: 0.8122 (p-80) cc_final: 0.7849 (p90) REVERT: A 309 PHE cc_start: 0.5142 (t80) cc_final: 0.4219 (t80) REVERT: A 456 TYR cc_start: 0.8566 (m-80) cc_final: 0.7589 (m-80) REVERT: A 489 MET cc_start: 0.9020 (ttp) cc_final: 0.8687 (mtm) REVERT: A 525 GLU cc_start: 0.8089 (pt0) cc_final: 0.7684 (pm20) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.4151 time to fit residues: 33.2070 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125203 restraints weight = 5156.402| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.43 r_work: 0.3384 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4642 Z= 0.150 Angle : 0.567 5.477 6367 Z= 0.269 Chirality : 0.039 0.263 730 Planarity : 0.004 0.036 734 Dihedral : 9.380 59.549 1063 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 18.76 % Favored : 79.25 % 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 are not related in a simple way. whole: 1.98 (0.36), residues: 536 helix: 2.02 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.43 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 530 TYR 0.016 0.001 TYR A 132 PHE 0.013 0.001 PHE A 91 TRP 0.010 0.001 TRP A 225 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4641) covalent geometry : angle 0.56685 / 0.27 ( 6365) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 0.28229 / 0.15 ( 2) hydrogen bonds : bond 0.04485 / 2.90 ( 290) hydrogen bonds : angle 4.46860 / 3.13 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.33 seconds wall clock time: 25 minutes 0.19 seconds (1500.19 seconds total)