Starting phenix.real_space_refine on Mon Jan 13 19:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfi_44497/01_2025/9bfi_44497.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.108 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 20 5.16 5 C 2523 2.51 5 N 566 2.21 5 O 657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3766 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 466} Chain breaks: 3 Time building chain proxies: 2.82, per 1000 atoms: 0.75 Number of scatterers: 3766 At special positions: 0 Unit cell: (75.276, 81.918, 72.324, 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 20 16.00 O 657 8.00 N 566 7.00 C 2523 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: 0.85 Conformation dependent library (CDL) restraints added in 428.6 milliseconds 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 1 sheets defined 77.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.763A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.594A pdb=" N THR A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 85 through 102 removed outlier: 4.682A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 157 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.772A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.111A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.920A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 298 removed outlier: 3.593A pdb=" N ILE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.659A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.554A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.613A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 271 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.01 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: 1088 1.34 - 1.46: 1025 1.46 - 1.58: 1726 1.58 - 1.70: 0 1.70 - 1.81: 35 Bond restraints: 3874 Sorted by residual: bond pdb=" C LYS A 226 " pdb=" N PRO A 227 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.30e-02 5.92e+03 2.38e+00 bond pdb=" C ILE A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.47e+00 bond pdb=" C ASP A 116 " pdb=" N PRO A 117 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.36e-02 5.41e+03 1.27e+00 bond pdb=" C ILE A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.20e+00 bond pdb=" C LEU A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.09e+00 ... (remaining 3869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5171 1.99 - 3.98: 103 3.98 - 5.97: 15 5.97 - 7.96: 2 7.96 - 9.95: 2 Bond angle restraints: 5293 Sorted by residual: angle pdb=" CA PRO A 105 " pdb=" N PRO A 105 " pdb=" CD PRO A 105 " ideal model delta sigma weight residual 112.00 107.29 4.71 1.40e+00 5.10e-01 1.13e+01 angle pdb=" CA LEU A 115 " pdb=" CB LEU A 115 " pdb=" CG LEU A 115 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.09e+00 angle pdb=" C ILE A 157 " pdb=" N ASP A 158 " pdb=" CA ASP A 158 " ideal model delta sigma weight residual 123.47 127.44 -3.97 1.53e+00 4.27e-01 6.74e+00 angle pdb=" CA MET A 358 " pdb=" CB MET A 358 " pdb=" CG MET A 358 " ideal model delta sigma weight residual 114.10 119.13 -5.03 2.00e+00 2.50e-01 6.33e+00 angle pdb=" C SER A 333 " pdb=" N PHE A 334 " pdb=" CA PHE A 334 " ideal model delta sigma weight residual 120.28 123.29 -3.01 1.34e+00 5.57e-01 5.05e+00 ... (remaining 5288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 1989 15.05 - 30.11: 157 30.11 - 45.16: 39 45.16 - 60.22: 4 60.22 - 75.27: 4 Dihedral angle restraints: 2193 sinusoidal: 786 harmonic: 1407 Sorted by residual: dihedral pdb=" CA GLY A 338 " pdb=" C GLY A 338 " pdb=" N ALA A 339 " pdb=" CA ALA A 339 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 100 " pdb=" C LEU A 100 " pdb=" N PHE A 101 " pdb=" CA PHE A 101 " ideal model delta harmonic sigma weight residual 180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 260 " pdb=" CB ARG A 260 " pdb=" CG ARG A 260 " pdb=" CD ARG A 260 " ideal model delta sinusoidal sigma weight residual 180.00 131.27 48.73 3 1.50e+01 4.44e-03 8.68e+00 ... (remaining 2190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 393 0.031 - 0.062: 150 0.062 - 0.093: 49 0.093 - 0.124: 19 0.124 - 0.155: 6 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA LYS A 104 " pdb=" N LYS A 104 " pdb=" C LYS A 104 " pdb=" CB LYS A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CB ILE A 156 " pdb=" CA ILE A 156 " pdb=" CG1 ILE A 156 " pdb=" CG2 ILE A 156 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA LEU A 320 " pdb=" N LEU A 320 " pdb=" C LEU A 320 " pdb=" CB LEU A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 614 not shown) Planarity restraints: 640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 104 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO A 105 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 338 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C GLY A 338 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY A 338 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 339 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 310 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.024 5.00e-02 4.00e+02 ... (remaining 637 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 965 2.80 - 3.32: 3655 3.32 - 3.85: 6450 3.85 - 4.37: 7316 4.37 - 4.90: 12983 Nonbonded interactions: 31369 Sorted by model distance: nonbonded pdb=" OH TYR A 433 " pdb=" OD1 ASP A 512 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OG SER A 410 " model vdw 2.283 3.040 nonbonded pdb=" NH2 ARG A 446 " pdb=" OE1 GLU A 451 " model vdw 2.292 3.120 nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.294 3.040 nonbonded pdb=" NH1 ARG A 107 " pdb=" O SER A 264 " model vdw 2.358 3.120 ... (remaining 31364 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: 0.590 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3874 Z= 0.228 Angle : 0.682 9.952 5293 Z= 0.375 Chirality : 0.040 0.155 617 Planarity : 0.007 0.121 640 Dihedral : 12.283 75.274 1301 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.36), residues: 481 helix: 0.67 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.77 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.016 0.001 PHE A 514 TYR 0.010 0.001 TYR A 439 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.348 Fit side-chains REVERT: A 114 MET cc_start: 0.7669 (tmm) cc_final: 0.7301 (tmm) REVERT: A 255 GLN cc_start: 0.6973 (tp-100) cc_final: 0.6752 (tp40) REVERT: A 335 PHE cc_start: 0.6829 (m-80) cc_final: 0.5870 (t80) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.8568 time to fit residues: 51.2299 Evaluate side-chains 43 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 191 GLN A 255 GLN A 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133661 restraints weight = 4232.748| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.95 r_work: 0.3415 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3874 Z= 0.197 Angle : 0.541 6.719 5293 Z= 0.282 Chirality : 0.037 0.125 617 Planarity : 0.006 0.077 640 Dihedral : 4.170 20.267 523 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.52 % Allowed : 5.57 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.37), residues: 481 helix: 1.25 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.42 (0.55), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 140 TYR 0.011 0.001 TYR A 80 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.354 Fit side-chains REVERT: A 114 MET cc_start: 0.7320 (tmm) cc_final: 0.7034 (tmm) REVERT: A 335 PHE cc_start: 0.6685 (m-80) cc_final: 0.5397 (t80) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.8839 time to fit residues: 48.2494 Evaluate side-chains 47 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 234 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132910 restraints weight = 4246.523| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.96 r_work: 0.3383 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.204 Angle : 0.525 5.932 5293 Z= 0.275 Chirality : 0.038 0.146 617 Planarity : 0.005 0.061 640 Dihedral : 4.103 19.433 523 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.52 % Allowed : 8.61 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.38), residues: 481 helix: 1.34 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS A 4 PHE 0.012 0.001 PHE A 334 TYR 0.011 0.001 TYR A 67 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.421 Fit side-chains REVERT: A 255 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.5622 (tm130) REVERT: A 335 PHE cc_start: 0.6701 (m-80) cc_final: 0.5374 (t80) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.9412 time to fit residues: 50.3717 Evaluate side-chains 51 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 255 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.175280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132497 restraints weight = 4239.901| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.95 r_work: 0.3375 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3874 Z= 0.212 Angle : 0.520 5.966 5293 Z= 0.273 Chirality : 0.038 0.142 617 Planarity : 0.005 0.051 640 Dihedral : 4.095 19.328 523 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.78 % Allowed : 8.61 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 481 helix: 1.36 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.012 0.001 PHE A 334 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.313 Fit side-chains REVERT: A 335 PHE cc_start: 0.6727 (m-80) cc_final: 0.5410 (t80) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.8474 time to fit residues: 44.4703 Evaluate side-chains 48 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 19 optimal weight: 0.0040 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.176134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133020 restraints weight = 4321.214| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.98 r_work: 0.3386 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3874 Z= 0.180 Angle : 0.496 6.005 5293 Z= 0.259 Chirality : 0.037 0.130 617 Planarity : 0.004 0.043 640 Dihedral : 4.013 18.856 523 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.28 % Allowed : 11.14 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.38), residues: 481 helix: 1.51 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.38 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.011 0.001 PHE A 334 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.378 Fit side-chains REVERT: A 156 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6694 (tp) REVERT: A 335 PHE cc_start: 0.6748 (m-80) cc_final: 0.5432 (t80) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.8900 time to fit residues: 44.8113 Evaluate side-chains 48 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 313 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135126 restraints weight = 4248.550| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.96 r_work: 0.3425 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3874 Z= 0.151 Angle : 0.477 6.020 5293 Z= 0.250 Chirality : 0.036 0.120 617 Planarity : 0.004 0.036 640 Dihedral : 3.903 18.485 523 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.03 % Allowed : 11.65 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.38), residues: 481 helix: 1.70 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.29 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.014 0.001 PHE A 386 TYR 0.010 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.397 Fit side-chains REVERT: A 156 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6654 (tp) REVERT: A 335 PHE cc_start: 0.6689 (m-80) cc_final: 0.5398 (t80) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.8231 time to fit residues: 44.2174 Evaluate side-chains 47 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 255 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.172248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129150 restraints weight = 4238.889| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.96 r_work: 0.3315 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3874 Z= 0.326 Angle : 0.587 6.404 5293 Z= 0.308 Chirality : 0.041 0.226 617 Planarity : 0.005 0.039 640 Dihedral : 4.223 19.178 523 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.66 % Favored : 98.13 % Rotamer: Outliers : 2.78 % Allowed : 11.14 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.38), residues: 481 helix: 1.25 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.42 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.002 0.001 HIS A 4 PHE 0.016 0.002 PHE A 334 TYR 0.013 0.002 TYR A 67 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.406 Fit side-chains REVERT: A 156 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6806 (tp) REVERT: A 335 PHE cc_start: 0.6812 (m-80) cc_final: 0.5513 (t80) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.8953 time to fit residues: 43.2875 Evaluate side-chains 47 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 412 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131907 restraints weight = 4286.891| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.99 r_work: 0.3393 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3874 Z= 0.198 Angle : 0.513 6.071 5293 Z= 0.268 Chirality : 0.037 0.141 617 Planarity : 0.004 0.035 640 Dihedral : 4.074 18.671 523 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.87 % Favored : 97.92 % Rotamer: Outliers : 2.03 % Allowed : 12.15 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.38), residues: 481 helix: 1.47 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.35 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.012 0.001 PHE A 131 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.409 Fit side-chains REVERT: A 156 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6717 (tp) REVERT: A 335 PHE cc_start: 0.6792 (m-80) cc_final: 0.5467 (t80) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.8740 time to fit residues: 44.0424 Evaluate side-chains 50 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 255 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 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 119 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133689 restraints weight = 4169.191| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.95 r_work: 0.3350 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3874 Z= 0.183 Angle : 0.512 6.059 5293 Z= 0.267 Chirality : 0.037 0.133 617 Planarity : 0.004 0.033 640 Dihedral : 4.009 18.590 523 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.87 % Favored : 97.92 % Rotamer: Outliers : 2.03 % Allowed : 12.66 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.38), residues: 481 helix: 1.58 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.31 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS A 221 PHE 0.013 0.001 PHE A 131 TYR 0.010 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.374 Fit side-chains REVERT: A 156 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6691 (tp) REVERT: A 223 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7507 (ttmt) REVERT: A 335 PHE cc_start: 0.6741 (m-80) cc_final: 0.5455 (t80) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.8559 time to fit residues: 48.5987 Evaluate side-chains 52 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 255 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 0.0010 chunk 28 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135050 restraints weight = 4232.799| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.97 r_work: 0.3407 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3874 Z= 0.147 Angle : 0.497 6.037 5293 Z= 0.257 Chirality : 0.036 0.119 617 Planarity : 0.004 0.031 640 Dihedral : 3.920 18.379 523 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.08 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 13.42 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.39), residues: 481 helix: 1.75 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.24 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.001 0.000 HIS A 4 PHE 0.013 0.001 PHE A 131 TYR 0.010 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 962 Ramachandran restraints generated. 481 Oldfield, 0 Emsley, 481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.399 Fit side-chains REVERT: A 156 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6671 (tp) REVERT: A 223 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7542 (ttmt) REVERT: A 335 PHE cc_start: 0.6721 (m-80) cc_final: 0.5411 (t80) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.9385 time to fit residues: 47.1720 Evaluate side-chains 48 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 255 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133766 restraints weight = 4213.002| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.97 r_work: 0.3407 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3874 Z= 0.177 Angle : 0.518 6.881 5293 Z= 0.269 Chirality : 0.037 0.133 617 Planarity : 0.004 0.032 640 Dihedral : 3.951 18.742 523 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.08 % Favored : 97.71 % Rotamer: Outliers : 0.76 % Allowed : 14.18 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.38), residues: 481 helix: 1.72 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -0.19 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 4 PHE 0.015 0.001 PHE A 386 TYR 0.011 0.001 TYR A 67 ARG 0.001 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.60 seconds wall clock time: 53 minutes 31.15 seconds (3211.15 seconds total)