Starting phenix.real_space_refine on Fri Aug 22 13:25:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtt_36652/08_2025/8jtt_36652.map" } resolution = 3.87 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= 0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2182 2.51 5 N 534 2.21 5 O 584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3312 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 20, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.17, per 1000 atoms: 0.35 Number of scatterers: 3321 At special positions: 0 Unit cell: (85.5175, 58.455, 64.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 584 8.00 N 534 7.00 C 2182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 138.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 4.023A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 143 through 173 removed outlier: 3.515A pdb=" N LEU A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.724A pdb=" N PHE A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.704A pdb=" N VAL A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 removed outlier: 3.907A pdb=" N LEU A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.794A pdb=" N GLU A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.146A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 339 through 367 removed outlier: 5.596A pdb=" N LYS A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.749A pdb=" N GLY A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.702A pdb=" N CYS A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.962A pdb=" N LEU A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.917A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 696 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: 0.52 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1031 1.34 - 1.46: 712 1.46 - 1.58: 1625 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3400 Sorted by residual: bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.439 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.252 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C04 MF8 A 601 " pdb=" N02 MF8 A 601 " ideal model delta sigma weight residual 1.362 1.448 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.444 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.387 1.454 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4470 1.92 - 3.85: 157 3.85 - 5.77: 19 5.77 - 7.69: 12 7.69 - 9.62: 3 Bond angle restraints: 4661 Sorted by residual: angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 126.24 116.62 9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N02 MF8 A 601 " pdb=" C04 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 113.43 122.89 -9.46 3.00e+00 1.11e-01 9.93e+00 angle pdb=" N ARG A 439 " pdb=" CA ARG A 439 " pdb=" C ARG A 439 " ideal model delta sigma weight residual 111.07 107.88 3.19 1.07e+00 8.73e-01 8.88e+00 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.14 113.92 -2.78 1.08e+00 8.57e-01 6.62e+00 angle pdb=" C VAL A 212 " pdb=" CA VAL A 212 " pdb=" CB VAL A 212 " ideal model delta sigma weight residual 112.22 108.70 3.52 1.38e+00 5.25e-01 6.52e+00 ... (remaining 4656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 1766 16.55 - 33.10: 150 33.10 - 49.65: 31 49.65 - 66.20: 0 66.20 - 82.75: 1 Dihedral angle restraints: 1948 sinusoidal: 648 harmonic: 1300 Sorted by residual: dihedral pdb=" CA THR A 396 " pdb=" C THR A 396 " pdb=" N ILE A 397 " pdb=" CA ILE A 397 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU A 521 " pdb=" C LEU A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU A 27 " pdb=" C LEU A 27 " pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 414 0.048 - 0.097: 116 0.097 - 0.145: 29 0.145 - 0.193: 2 0.193 - 0.241: 4 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 562 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.222 2.00e-02 2.50e+03 3.51e-01 2.78e+03 pdb=" C03 MF8 A 601 " -0.138 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " 0.229 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " -0.097 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.043 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.587 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.083 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.325 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.723 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 271 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO A 283 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.027 5.00e-02 4.00e+02 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 752 2.78 - 3.31: 3285 3.31 - 3.84: 5585 3.84 - 4.37: 5758 4.37 - 4.90: 9929 Nonbonded interactions: 25309 Sorted by model distance: nonbonded pdb=" OG SER A 409 " pdb=" O GLY A 441 " model vdw 2.250 3.040 nonbonded pdb=" O PHE A 22 " pdb=" OH TYR A 240 " model vdw 2.252 3.040 nonbonded pdb=" O LEU A 42 " pdb=" OG SER A 133 " model vdw 2.348 3.040 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.357 3.040 nonbonded pdb=" OG SER A 189 " pdb=" OE1 GLN A 209 " model vdw 2.391 3.040 ... (remaining 25304 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.020 Set scattering table: 0.010 Process input model: 5.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.158 3400 Z= 0.300 Angle : 0.869 9.617 4661 Z= 0.444 Chirality : 0.049 0.241 565 Planarity : 0.016 0.351 581 Dihedral : 12.926 82.753 1112 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.35), residues: 450 helix: -0.51 (0.26), residues: 327 sheet: None (None), residues: 0 loop : -3.46 (0.45), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.015 0.001 TYR A 240 PHE 0.027 0.002 PHE A 482 TRP 0.011 0.001 TRP A 217 HIS 0.002 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 3400) covalent geometry : angle 0.86933 ( 4661) hydrogen bonds : bond 0.09979 ( 236) hydrogen bonds : angle 5.79174 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0454 time to fit residues: 4.4808 Evaluate side-chains 54 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 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 = 0.5440 r_free = 0.5440 target = 0.301344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.271544 restraints weight = 3828.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.277165 restraints weight = 2375.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.281041 restraints weight = 1693.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.283104 restraints weight = 1324.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.285175 restraints weight = 1123.399| |-----------------------------------------------------------------------------| r_work (final): 0.5393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.146 Angle : 0.597 9.951 4661 Z= 0.306 Chirality : 0.039 0.140 565 Planarity : 0.005 0.049 581 Dihedral : 4.375 16.451 475 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 8.31 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.38), residues: 450 helix: 0.29 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -3.40 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.010 0.001 TYR A 199 PHE 0.010 0.001 PHE A 22 TRP 0.017 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3400) covalent geometry : angle 0.59707 ( 4661) hydrogen bonds : bond 0.04541 ( 236) hydrogen bonds : angle 4.58736 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.120 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0386 time to fit residues: 3.3517 Evaluate side-chains 59 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 0.0050 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.5504 r_free = 0.5504 target = 0.307638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.278902 restraints weight = 3780.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5295 r_free = 0.5295 target = 0.284418 restraints weight = 2307.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.287644 restraints weight = 1625.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.290705 restraints weight = 1282.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.292023 restraints weight = 1056.320| |-----------------------------------------------------------------------------| r_work (final): 0.5392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3400 Z= 0.134 Angle : 0.566 9.546 4661 Z= 0.288 Chirality : 0.038 0.139 565 Planarity : 0.004 0.045 581 Dihedral : 4.185 14.999 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.46 % Allowed : 13.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.40), residues: 450 helix: 0.65 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -3.13 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.007 0.001 TYR A 240 PHE 0.011 0.001 PHE A 22 TRP 0.019 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3400) covalent geometry : angle 0.56608 ( 4661) hydrogen bonds : bond 0.04206 ( 236) hydrogen bonds : angle 4.41097 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.129 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.0404 time to fit residues: 3.4574 Evaluate side-chains 60 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 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 = 0.5441 r_free = 0.5441 target = 0.299700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.270121 restraints weight = 3821.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.275654 restraints weight = 2342.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.279111 restraints weight = 1651.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.281090 restraints weight = 1302.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.283082 restraints weight = 1112.992| |-----------------------------------------------------------------------------| r_work (final): 0.5327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3400 Z= 0.159 Angle : 0.607 9.169 4661 Z= 0.313 Chirality : 0.039 0.154 565 Planarity : 0.005 0.046 581 Dihedral : 4.346 15.754 475 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.00 % Allowed : 16.92 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.40), residues: 450 helix: 0.69 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.85 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.010 0.001 TYR A 240 PHE 0.025 0.002 PHE A 151 TRP 0.023 0.001 TRP A 261 HIS 0.005 0.002 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3400) covalent geometry : angle 0.60702 ( 4661) hydrogen bonds : bond 0.04809 ( 236) hydrogen bonds : angle 4.60259 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.127 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.0479 time to fit residues: 4.5385 Evaluate side-chains 64 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.5379 r_free = 0.5379 target = 0.293844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.265422 restraints weight = 3905.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.271000 restraints weight = 2381.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.274153 restraints weight = 1671.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.277490 restraints weight = 1317.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.278949 restraints weight = 1073.101| |-----------------------------------------------------------------------------| r_work (final): 0.5339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3400 Z= 0.144 Angle : 0.590 9.139 4661 Z= 0.300 Chirality : 0.038 0.152 565 Planarity : 0.004 0.047 581 Dihedral : 4.210 14.952 475 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 21.23 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.40), residues: 450 helix: 0.77 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.77 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.007 0.001 TYR A 199 PHE 0.010 0.001 PHE A 499 TRP 0.023 0.001 TRP A 261 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3400) covalent geometry : angle 0.59049 ( 4661) hydrogen bonds : bond 0.04508 ( 236) hydrogen bonds : angle 4.50737 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.123 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.0397 time to fit residues: 3.5072 Evaluate side-chains 62 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.5441 r_free = 0.5441 target = 0.299224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.270550 restraints weight = 3802.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.275803 restraints weight = 2232.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.278840 restraints weight = 1572.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.281391 restraints weight = 1244.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.283607 restraints weight = 1044.504| |-----------------------------------------------------------------------------| r_work (final): 0.5291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3400 Z= 0.148 Angle : 0.602 9.008 4661 Z= 0.304 Chirality : 0.038 0.139 565 Planarity : 0.004 0.047 581 Dihedral : 4.234 16.553 475 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.31 % Allowed : 19.69 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.40), residues: 450 helix: 0.80 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -2.80 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.007 0.001 TYR A 240 PHE 0.029 0.002 PHE A 151 TRP 0.029 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3400) covalent geometry : angle 0.60218 ( 4661) hydrogen bonds : bond 0.04563 ( 236) hydrogen bonds : angle 4.53126 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.100 Fit side-chains REVERT: A 173 PHE cc_start: 0.4784 (OUTLIER) cc_final: 0.4370 (m-10) REVERT: A 260 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.7003 (t-90) outliers start: 14 outliers final: 11 residues processed: 66 average time/residue: 0.0352 time to fit residues: 3.3682 Evaluate side-chains 70 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 479 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.5467 r_free = 0.5467 target = 0.302736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.274753 restraints weight = 3877.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.280006 restraints weight = 2280.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.283124 restraints weight = 1597.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.285986 restraints weight = 1257.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.288257 restraints weight = 1028.217| |-----------------------------------------------------------------------------| r_work (final): 0.5321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.129 Angle : 0.573 9.084 4661 Z= 0.286 Chirality : 0.037 0.132 565 Planarity : 0.004 0.046 581 Dihedral : 4.073 15.392 475 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.69 % Allowed : 22.15 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.41), residues: 450 helix: 0.98 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.68 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.006 0.001 TYR A 199 PHE 0.029 0.001 PHE A 151 TRP 0.034 0.001 TRP A 261 HIS 0.001 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3400) covalent geometry : angle 0.57252 ( 4661) hydrogen bonds : bond 0.04165 ( 236) hydrogen bonds : angle 4.43918 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.119 Fit side-chains REVERT: A 173 PHE cc_start: 0.4764 (OUTLIER) cc_final: 0.4273 (m-10) outliers start: 12 outliers final: 11 residues processed: 66 average time/residue: 0.0414 time to fit residues: 3.8596 Evaluate side-chains 68 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.5390 r_free = 0.5390 target = 0.295578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.268062 restraints weight = 4006.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.273774 restraints weight = 2397.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.277028 restraints weight = 1641.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.279204 restraints weight = 1273.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.281835 restraints weight = 1066.899| |-----------------------------------------------------------------------------| r_work (final): 0.5289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.130 Angle : 0.575 9.065 4661 Z= 0.287 Chirality : 0.037 0.125 565 Planarity : 0.004 0.046 581 Dihedral : 4.021 14.967 475 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.69 % Allowed : 23.08 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.41), residues: 450 helix: 1.04 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.65 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.005 0.001 TYR A 199 PHE 0.009 0.001 PHE A 499 TRP 0.036 0.001 TRP A 261 HIS 0.001 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3400) covalent geometry : angle 0.57452 ( 4661) hydrogen bonds : bond 0.04156 ( 236) hydrogen bonds : angle 4.40025 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.126 Fit side-chains REVERT: A 173 PHE cc_start: 0.4645 (OUTLIER) cc_final: 0.4212 (m-10) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.0360 time to fit residues: 3.3990 Evaluate side-chains 68 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 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 = 0.5346 r_free = 0.5346 target = 0.289763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.261609 restraints weight = 3968.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.267076 restraints weight = 2361.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.270103 restraints weight = 1643.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.272890 restraints weight = 1299.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.273850 restraints weight = 1088.848| |-----------------------------------------------------------------------------| r_work (final): 0.5071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3400 Z= 0.159 Angle : 0.614 9.015 4661 Z= 0.312 Chirality : 0.039 0.147 565 Planarity : 0.004 0.047 581 Dihedral : 4.199 15.353 475 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 24.00 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.41), residues: 450 helix: 0.84 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.68 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.006 0.001 TYR A 199 PHE 0.030 0.002 PHE A 151 TRP 0.039 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3400) covalent geometry : angle 0.61375 ( 4661) hydrogen bonds : bond 0.04761 ( 236) hydrogen bonds : angle 4.61838 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.117 Fit side-chains REVERT: A 173 PHE cc_start: 0.5050 (OUTLIER) cc_final: 0.4803 (m-10) REVERT: A 218 MET cc_start: 0.7428 (tpt) cc_final: 0.7208 (tpt) REVERT: A 384 LEU cc_start: 0.7392 (tp) cc_final: 0.7077 (tp) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.0386 time to fit residues: 3.5981 Evaluate side-chains 69 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 0.0770 chunk 4 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 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 = 0.5230 r_free = 0.5230 target = 0.281232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.254119 restraints weight = 3972.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.259715 restraints weight = 2261.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.262855 restraints weight = 1519.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.265676 restraints weight = 1163.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.267894 restraints weight = 935.970| |-----------------------------------------------------------------------------| r_work (final): 0.5348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3400 Z= 0.127 Angle : 0.579 9.044 4661 Z= 0.289 Chirality : 0.037 0.116 565 Planarity : 0.004 0.047 581 Dihedral : 3.953 15.091 475 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.38 % Allowed : 25.23 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.41), residues: 450 helix: 1.07 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -2.55 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.006 0.001 TYR A 240 PHE 0.027 0.001 PHE A 151 TRP 0.037 0.001 TRP A 261 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3400) covalent geometry : angle 0.57916 ( 4661) hydrogen bonds : bond 0.04062 ( 236) hydrogen bonds : angle 4.36016 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.117 Fit side-chains REVERT: A 173 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.4292 (m-10) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.0374 time to fit residues: 3.4189 Evaluate side-chains 65 residues out of total 382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 TRP Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 461 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** 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 = 0.5356 r_free = 0.5356 target = 0.291214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.264058 restraints weight = 3986.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.269067 restraints weight = 2299.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.272070 restraints weight = 1601.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.274715 restraints weight = 1265.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.275962 restraints weight = 1067.464| |-----------------------------------------------------------------------------| r_work (final): 0.5327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3400 Z= 0.146 Angle : 0.614 9.025 4661 Z= 0.309 Chirality : 0.038 0.130 565 Planarity : 0.004 0.046 581 Dihedral : 4.053 15.137 475 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 25.85 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.41), residues: 450 helix: 0.97 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -2.58 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 206 TYR 0.014 0.001 TYR A 240 PHE 0.026 0.002 PHE A 151 TRP 0.039 0.001 TRP A 261 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3400) covalent geometry : angle 0.61443 ( 4661) hydrogen bonds : bond 0.04543 ( 236) hydrogen bonds : angle 4.49343 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 724.24 seconds wall clock time: 13 minutes 8.01 seconds (788.01 seconds total)