Starting phenix.real_space_refine on Sat Apr 4 22:06:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmp_66100/04_2026/9wmp_66100.map" } resolution = 2.91 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= 0.103 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 3019 2.51 5 N 657 2.21 5 O 721 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4433 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: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 1.26, per 1000 atoms: 0.28 Number of scatterers: 4433 At special positions: 0 Unit cell: (82.159, 69.355, 82.159, 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 721 8.00 N 657 7.00 C 3019 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: 0.31 Conformation dependent library (CDL) restraints added in 254.7 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: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.537A 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: 3.548A 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: 3.872A 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: 4.243A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.823A 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: 3.791A 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: 0.71 Time building geometry restraints manager: 0.40 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: 626 1.31 - 1.44: 1320 1.44 - 1.56: 2580 1.56 - 1.69: 2 1.69 - 1.81: 54 Bond restraints: 4582 Sorted by residual: bond pdb=" C SER A 381 " pdb=" O SER A 381 " ideal model delta sigma weight residual 1.238 1.186 0.051 1.28e-02 6.10e+03 1.62e+01 bond pdb=" N SER A 381 " pdb=" CA SER A 381 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.41e-02 5.03e+03 1.21e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.500 -0.040 1.19e-02 7.06e+03 1.11e+01 bond pdb=" C ILE A 479 " pdb=" O ILE A 479 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.32e-02 5.74e+03 1.08e+01 bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.496 -0.033 1.05e-02 9.07e+03 1.01e+01 ... (remaining 4577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 6004 2.14 - 4.28: 240 4.28 - 6.42: 32 6.42 - 8.56: 4 8.56 - 10.70: 1 Bond angle restraints: 6281 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 111.11 105.37 5.74 1.20e+00 6.94e-01 2.29e+01 angle pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" O LEU A 395 " ideal model delta sigma weight residual 120.82 116.33 4.49 1.05e+00 9.07e-01 1.83e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.05e+00 9.07e-01 1.58e+01 angle pdb=" CA LEU A 503 " pdb=" C LEU A 503 " pdb=" O LEU A 503 " ideal model delta sigma weight residual 120.42 116.31 4.11 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N MET A 135 " pdb=" CA MET A 135 " pdb=" C MET A 135 " ideal model delta sigma weight residual 111.71 107.30 4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 6276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 2627 23.98 - 47.95: 209 47.95 - 71.92: 36 71.92 - 95.90: 1 95.90 - 119.87: 13 Dihedral angle restraints: 2886 sinusoidal: 1336 harmonic: 1550 Sorted by residual: dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" O1 CLR A 707 " ideal model delta sinusoidal sigma weight residual 180.04 60.17 119.87 1 3.00e+01 1.11e-03 1.60e+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 62.25 -119.08 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 CLR A 707 " pdb=" C2 CLR A 707 " pdb=" C3 CLR A 707 " pdb=" C4 CLR A 707 " ideal model delta sinusoidal sigma weight residual 57.41 -61.45 118.86 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 2883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 534 0.044 - 0.089: 114 0.089 - 0.133: 57 0.133 - 0.177: 14 0.177 - 0.221: 3 Chirality restraints: 722 Sorted by residual: 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 1.23e+00 chirality pdb=" CA GLN A 400 " pdb=" N GLN A 400 " pdb=" C GLN A 400 " pdb=" CB GLN A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 719 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 321 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.35e+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 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 402 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ALA A 402 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 402 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.044 5.00e-02 4.00e+02 6.56e-02 6.89e+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 " 0.036 5.00e-02 4.00e+02 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1556 2.86 - 3.37: 4465 3.37 - 3.88: 7916 3.88 - 4.39: 9598 4.39 - 4.90: 15541 Nonbonded interactions: 39076 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 2.470 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 2.470 nonbonded pdb=" O PHE A 339 " pdb=" OG SER A 343 " model vdw 2.433 3.040 ... (remaining 39071 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: 1.140 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.110 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:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 4583 Z= 0.356 Angle : 0.891 10.699 6283 Z= 0.560 Chirality : 0.049 0.221 722 Planarity : 0.007 0.066 726 Dihedral : 18.705 119.873 1901 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.35), residues: 536 helix: 0.86 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00535 ( 4582) covalent geometry : angle 0.89127 ( 6281) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.51859 ( 2) hydrogen bonds : bond 0.12732 ( 290) hydrogen bonds : angle 6.03806 ( 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 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.172 Fit side-chains REVERT: A 312 TYR cc_start: 0.8058 (m-80) cc_final: 0.7745 (m-80) REVERT: A 358 GLN cc_start: 0.7820 (pt0) cc_final: 0.7548 (pp30) REVERT: A 414 GLU cc_start: 0.7565 (tp30) cc_final: 0.7355 (tp30) outliers start: 0 outliers final: 1 residues processed: 91 average time/residue: 0.5391 time to fit residues: 50.8394 Evaluate side-chains 57 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122026 restraints weight = 5321.780| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.48 r_work: 0.3179 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4583 Z= 0.141 Angle : 0.611 6.196 6283 Z= 0.289 Chirality : 0.039 0.176 722 Planarity : 0.005 0.056 726 Dihedral : 9.124 57.818 976 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.53 % Allowed : 17.44 % Favored : 79.03 % 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: 1.44 (0.36), residues: 536 helix: 1.80 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.06 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 568 TYR 0.018 0.001 TYR A 132 PHE 0.015 0.001 PHE A 245 TRP 0.013 0.001 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4582) covalent geometry : angle 0.61107 ( 6281) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.38298 ( 2) hydrogen bonds : bond 0.04413 ( 290) hydrogen bonds : angle 4.67560 ( 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 84 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8296 (tpt) cc_final: 0.7643 (tpt) REVERT: A 191 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 312 TYR cc_start: 0.8368 (m-80) cc_final: 0.7899 (m-80) REVERT: A 332 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 348 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8134 (mtp) REVERT: A 357 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7648 (p0) REVERT: A 358 GLN cc_start: 0.8203 (pt0) cc_final: 0.7557 (pm20) REVERT: A 414 GLU cc_start: 0.7611 (tp30) cc_final: 0.7349 (tp30) REVERT: A 525 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 571 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (mp10) outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 0.4512 time to fit residues: 36.7450 Evaluate side-chains 69 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.139265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121924 restraints weight = 5344.103| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.45 r_work: 0.3168 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4583 Z= 0.144 Angle : 0.545 5.577 6283 Z= 0.264 Chirality : 0.039 0.182 722 Planarity : 0.004 0.047 726 Dihedral : 8.238 59.756 974 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.53 % Allowed : 18.10 % 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: 1.77 (0.36), residues: 536 helix: 2.04 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.93 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 568 TYR 0.019 0.001 TYR A 132 PHE 0.010 0.001 PHE A 303 TRP 0.010 0.001 TRP A 225 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4582) covalent geometry : angle 0.54528 ( 6281) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.33970 ( 2) hydrogen bonds : bond 0.04436 ( 290) hydrogen bonds : angle 4.55921 ( 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 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: A 312 TYR cc_start: 0.8439 (m-80) cc_final: 0.8078 (m-80) REVERT: A 348 MET cc_start: 0.8512 (mtm) cc_final: 0.8178 (mtp) REVERT: A 358 GLN cc_start: 0.8335 (pt0) cc_final: 0.7992 (pt0) REVERT: A 525 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 544 LEU cc_start: 0.7698 (tp) cc_final: 0.7442 (tp) REVERT: A 555 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 571 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7980 (mp10) outliers start: 16 outliers final: 4 residues processed: 70 average time/residue: 0.4493 time to fit residues: 32.8987 Evaluate side-chains 67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114801 restraints weight = 5370.154| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.52 r_work: 0.3137 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4583 Z= 0.135 Angle : 0.520 5.355 6283 Z= 0.252 Chirality : 0.038 0.163 722 Planarity : 0.004 0.039 726 Dihedral : 8.192 56.194 974 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.53 % Allowed : 18.54 % 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: 1.92 (0.36), residues: 536 helix: 2.17 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.93 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.018 0.001 TYR A 132 PHE 0.010 0.001 PHE A 303 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4582) covalent geometry : angle 0.52031 ( 6281) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.19306 ( 2) hydrogen bonds : bond 0.04233 ( 290) hydrogen bonds : angle 4.47287 ( 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 82 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8027 (mp) cc_final: 0.7701 (tt) REVERT: A 312 TYR cc_start: 0.8638 (m-80) cc_final: 0.8288 (m-80) REVERT: A 332 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 358 GLN cc_start: 0.8269 (pt0) cc_final: 0.8014 (pt0) REVERT: A 516 TYR cc_start: 0.8373 (m-80) cc_final: 0.8127 (m-80) REVERT: A 525 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 555 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 571 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (mp10) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.4776 time to fit residues: 37.3266 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115472 restraints weight = 5430.268| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.63 r_work: 0.3106 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4583 Z= 0.140 Angle : 0.527 5.325 6283 Z= 0.254 Chirality : 0.038 0.160 722 Planarity : 0.004 0.035 726 Dihedral : 8.103 54.182 974 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.53 % Allowed : 20.75 % Favored : 75.72 % 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: 2.25 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.83 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.018 0.001 TYR A 132 PHE 0.011 0.001 PHE A 303 TRP 0.009 0.001 TRP A 225 HIS 0.003 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4582) covalent geometry : angle 0.52712 ( 6281) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.18562 ( 2) hydrogen bonds : bond 0.04216 ( 290) hydrogen bonds : angle 4.43510 ( 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 80 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8583 (mmm) cc_final: 0.8380 (mmm) REVERT: A 85 ILE cc_start: 0.7963 (mp) cc_final: 0.7623 (tt) REVERT: A 191 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: A 312 TYR cc_start: 0.8675 (m-80) cc_final: 0.8225 (m-80) REVERT: A 358 GLN cc_start: 0.8263 (pt0) cc_final: 0.8038 (pt0) REVERT: A 516 TYR cc_start: 0.8316 (m-80) cc_final: 0.8078 (m-80) REVERT: A 525 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 555 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7373 (tp) REVERT: A 571 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7914 (mp10) outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.4939 time to fit residues: 38.1071 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128540 restraints weight = 5445.878| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.49 r_work: 0.3133 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4583 Z= 0.133 Angle : 0.518 5.287 6283 Z= 0.250 Chirality : 0.039 0.158 722 Planarity : 0.004 0.033 726 Dihedral : 7.907 51.525 974 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.75 % Allowed : 20.09 % Favored : 76.16 % 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: 2.08 (0.36), residues: 536 helix: 2.26 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.78 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.018 0.001 TYR A 132 PHE 0.011 0.001 PHE A 303 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4582) covalent geometry : angle 0.51773 ( 6281) SS BOND : bond 0.00014 ( 1) SS BOND : angle 0.14737 ( 2) hydrogen bonds : bond 0.04120 ( 290) hydrogen bonds : angle 4.41111 ( 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 81 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8097 (mp) cc_final: 0.7758 (tt) REVERT: A 191 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: A 234 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7595 (mmtt) REVERT: A 312 TYR cc_start: 0.8633 (m-80) cc_final: 0.8241 (m-80) REVERT: A 516 TYR cc_start: 0.8360 (m-80) cc_final: 0.8098 (m-80) REVERT: A 525 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 555 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7497 (tp) REVERT: A 571 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (mp10) outliers start: 17 outliers final: 9 residues processed: 74 average time/residue: 0.4939 time to fit residues: 38.0875 Evaluate side-chains 75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129120 restraints weight = 5415.504| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.49 r_work: 0.3137 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4583 Z= 0.125 Angle : 0.518 5.258 6283 Z= 0.251 Chirality : 0.038 0.165 722 Planarity : 0.004 0.033 726 Dihedral : 7.788 52.049 974 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.31 % Allowed : 21.19 % Favored : 75.50 % 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: 2.14 (0.36), residues: 536 helix: 2.31 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.81 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.018 0.001 TYR A 132 PHE 0.009 0.001 PHE A 303 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4582) covalent geometry : angle 0.51856 ( 6281) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.15715 ( 2) hydrogen bonds : bond 0.04023 ( 290) hydrogen bonds : angle 4.36871 ( 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 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8139 (mp) cc_final: 0.7798 (tt) REVERT: A 191 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: A 234 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (mmtt) REVERT: A 312 TYR cc_start: 0.8627 (m-80) cc_final: 0.8261 (m-80) REVERT: A 377 MET cc_start: 0.8131 (mmm) cc_final: 0.7906 (mmm) REVERT: A 516 TYR cc_start: 0.8342 (m-80) cc_final: 0.8086 (m-80) REVERT: A 525 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 548 LEU cc_start: 0.7995 (mt) cc_final: 0.7742 (pp) REVERT: A 571 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7979 (mt0) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.4526 time to fit residues: 33.5562 Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.0040 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130191 restraints weight = 5361.817| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.48 r_work: 0.3150 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4583 Z= 0.117 Angle : 0.502 5.225 6283 Z= 0.243 Chirality : 0.038 0.147 722 Planarity : 0.004 0.033 726 Dihedral : 7.686 51.528 974 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 21.19 % Favored : 75.72 % 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: 2.16 (0.37), residues: 536 helix: 2.33 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.77 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.017 0.001 TYR A 132 PHE 0.009 0.001 PHE A 91 TRP 0.009 0.001 TRP A 225 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4582) covalent geometry : angle 0.50202 ( 6281) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.61206 ( 2) hydrogen bonds : bond 0.03953 ( 290) hydrogen bonds : angle 4.33875 ( 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: 14 poor density : 65 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8091 (mp) cc_final: 0.7675 (tt) REVERT: A 191 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: A 234 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7590 (mmtt) REVERT: A 312 TYR cc_start: 0.8618 (m-80) cc_final: 0.8305 (m-80) REVERT: A 516 TYR cc_start: 0.8338 (m-80) cc_final: 0.8085 (m-80) REVERT: A 549 MET cc_start: 0.8387 (ttm) cc_final: 0.8117 (ttt) REVERT: A 571 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7966 (mp10) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.4625 time to fit residues: 36.3530 Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127830 restraints weight = 5423.609| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.49 r_work: 0.3436 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4583 Z= 0.117 Angle : 0.510 5.235 6283 Z= 0.246 Chirality : 0.038 0.144 722 Planarity : 0.004 0.032 726 Dihedral : 7.602 51.467 974 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 22.52 % Favored : 74.39 % 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: 2.18 (0.36), residues: 536 helix: 2.32 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.76 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.017 0.001 TYR A 132 PHE 0.009 0.001 PHE A 460 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4582) covalent geometry : angle 0.50979 ( 6281) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.29085 ( 2) hydrogen bonds : bond 0.03926 ( 290) hydrogen bonds : angle 4.31873 ( 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 76 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8248 (mp) cc_final: 0.7917 (tt) REVERT: A 191 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: A 312 TYR cc_start: 0.8616 (m-80) cc_final: 0.8331 (m-80) REVERT: A 516 TYR cc_start: 0.8440 (m-80) cc_final: 0.8172 (m-80) REVERT: A 555 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7661 (tp) REVERT: A 571 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8094 (mt0) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.4784 time to fit residues: 35.9709 Evaluate side-chains 75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.146592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129817 restraints weight = 5357.340| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.48 r_work: 0.3153 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4583 Z= 0.123 Angle : 0.520 5.315 6283 Z= 0.250 Chirality : 0.038 0.144 722 Planarity : 0.004 0.032 726 Dihedral : 7.572 51.193 974 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.87 % Allowed : 22.74 % Favored : 74.39 % 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: 2.14 (0.36), residues: 536 helix: 2.29 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -0.75 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 420 TYR 0.018 0.001 TYR A 132 PHE 0.009 0.001 PHE A 460 TRP 0.008 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4582) covalent geometry : angle 0.52004 ( 6281) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.35145 ( 2) hydrogen bonds : bond 0.03971 ( 290) hydrogen bonds : angle 4.34081 ( 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 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: A 312 TYR cc_start: 0.8636 (m-80) cc_final: 0.8319 (m-80) REVERT: A 516 TYR cc_start: 0.8332 (m-80) cc_final: 0.8051 (m-80) REVERT: A 571 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7908 (mt0) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.4833 time to fit residues: 35.3347 Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 571 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114251 restraints weight = 5533.160| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3115 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4583 Z= 0.142 Angle : 0.567 11.977 6283 Z= 0.264 Chirality : 0.040 0.150 722 Planarity : 0.004 0.032 726 Dihedral : 7.614 50.944 974 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.09 % Allowed : 22.96 % Favored : 73.95 % 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: 2.07 (0.36), residues: 536 helix: 2.26 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.83 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.019 0.001 TYR A 132 PHE 0.013 0.001 PHE A 460 TRP 0.009 0.001 TRP A 225 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4582) covalent geometry : angle 0.56730 ( 6281) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.29228 ( 2) hydrogen bonds : bond 0.04109 ( 290) hydrogen bonds : angle 4.42960 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.20 seconds wall clock time: 28 minutes 25.89 seconds (1705.89 seconds total)