Starting phenix.real_space_refine on Wed Sep 17 09:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbi_61315/09_2025/9jbi_61315.map" } resolution = 4.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 40 5.16 5 C 4920 2.51 5 N 1188 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7472 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3736 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 19, 'TRANS': 497} Chain breaks: 9 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 15, 'GLN:plan1': 3, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "B" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3736 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 19, 'TRANS': 497} Chain breaks: 9 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 15, 'GLN:plan1': 3, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 169 Time building chain proxies: 1.91, per 1000 atoms: 0.26 Number of scatterers: 7472 At special positions: 0 Unit cell: (70.296, 175.336, 66.256, 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 40 16.00 O 1324 8.00 N 1188 7.00 C 4920 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: 0.64 Conformation dependent library (CDL) restraints added in 391.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 38 through 63 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.936A pdb=" N PHE A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.459A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.586A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.452A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.856A pdb=" N VAL A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.502A pdb=" N GLU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 326 through 337 removed outlier: 3.958A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 365 removed outlier: 3.527A pdb=" N ILE A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 404 Processing helix chain 'A' and resid 410 through 430 removed outlier: 4.067A pdb=" N LEU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.865A pdb=" N LEU A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.802A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 491' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 519 through 537 Processing helix chain 'A' and resid 655 through 682 removed outlier: 3.771A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 702 through 710 removed outlier: 3.588A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 63 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 66 through 79 Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 99 through 125 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.935A pdb=" N PHE B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.458A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.585A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.452A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.856A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.502A pdb=" N GLU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.958A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 365 removed outlier: 3.527A pdb=" N ILE B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 351 " --> pdb=" O MET B 347 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 373 through 404 Processing helix chain 'B' and resid 410 through 430 removed outlier: 4.067A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 472 removed outlier: 3.865A pdb=" N LEU B 450 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 491 removed outlier: 3.802A pdb=" N ILE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 491' Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 519 through 537 Processing helix chain 'B' and resid 655 through 682 removed outlier: 3.771A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 701 Processing helix chain 'B' and resid 702 through 710 removed outlier: 3.587A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1800 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: 1.24 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1182 1.32 - 1.44: 1962 1.44 - 1.57: 4410 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7614 Sorted by residual: bond pdb=" C ALA A 173 " pdb=" O ALA A 173 " ideal model delta sigma weight residual 1.238 1.199 0.039 1.28e-02 6.10e+03 9.23e+00 bond pdb=" C ALA B 173 " pdb=" O ALA B 173 " ideal model delta sigma weight residual 1.238 1.199 0.039 1.28e-02 6.10e+03 9.21e+00 bond pdb=" N ILE B 532 " pdb=" CA ILE B 532 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.30e-02 5.92e+03 8.30e+00 bond pdb=" N ILE A 706 " pdb=" CA ILE A 706 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" N ILE B 706 " pdb=" CA ILE B 706 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 7609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 8727 1.34 - 2.68: 1218 2.68 - 4.02: 328 4.02 - 5.36: 89 5.36 - 6.70: 26 Bond angle restraints: 10388 Sorted by residual: angle pdb=" N ASN A 315 " pdb=" CA ASN A 315 " pdb=" C ASN A 315 " ideal model delta sigma weight residual 111.36 105.79 5.57 1.09e+00 8.42e-01 2.61e+01 angle pdb=" N ASN B 315 " pdb=" CA ASN B 315 " pdb=" C ASN B 315 " ideal model delta sigma weight residual 111.36 105.79 5.57 1.09e+00 8.42e-01 2.61e+01 angle pdb=" N ALA B 134 " pdb=" CA ALA B 134 " pdb=" C ALA B 134 " ideal model delta sigma weight residual 112.92 106.83 6.09 1.23e+00 6.61e-01 2.45e+01 angle pdb=" N ALA A 134 " pdb=" CA ALA A 134 " pdb=" C ALA A 134 " ideal model delta sigma weight residual 112.92 106.86 6.06 1.23e+00 6.61e-01 2.42e+01 angle pdb=" N ILE A 522 " pdb=" CA ILE A 522 " pdb=" C ILE A 522 " ideal model delta sigma weight residual 110.74 106.54 4.20 9.10e-01 1.21e+00 2.13e+01 ... (remaining 10383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4076 17.44 - 34.87: 292 34.87 - 52.31: 52 52.31 - 69.74: 16 69.74 - 87.18: 6 Dihedral angle restraints: 4442 sinusoidal: 1460 harmonic: 2982 Sorted by residual: dihedral pdb=" CA MET B 179 " pdb=" C MET B 179 " pdb=" N LEU B 180 " pdb=" CA LEU B 180 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA MET A 179 " pdb=" C MET A 179 " pdb=" N LEU A 180 " pdb=" CA LEU A 180 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE B 431 " pdb=" C ILE B 431 " pdb=" N TRP B 432 " pdb=" CA TRP B 432 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 4439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 792 0.044 - 0.088: 317 0.088 - 0.133: 123 0.133 - 0.177: 40 0.177 - 0.221: 26 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA ILE B 534 " pdb=" N ILE B 534 " pdb=" C ILE B 534 " pdb=" CB ILE B 534 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE A 534 " pdb=" N ILE A 534 " pdb=" C ILE A 534 " pdb=" CB ILE A 534 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1295 not shown) Planarity restraints: 1274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 149 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C LEU B 149 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU B 149 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 149 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C LEU A 149 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 149 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY A 150 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 77 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C VAL A 77 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 77 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 78 " 0.012 2.00e-02 2.50e+03 ... (remaining 1271 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1117 2.76 - 3.29: 8965 3.29 - 3.83: 12649 3.83 - 4.36: 15552 4.36 - 4.90: 22939 Nonbonded interactions: 61222 Sorted by model distance: nonbonded pdb=" O PHE B 384 " pdb=" OG SER B 387 " model vdw 2.220 3.040 nonbonded pdb=" O PHE A 384 " pdb=" OG SER A 387 " model vdw 2.220 3.040 nonbonded pdb=" O MET A 347 " pdb=" OG SER A 350 " model vdw 2.275 3.040 nonbonded pdb=" O MET B 347 " pdb=" OG SER B 350 " model vdw 2.275 3.040 nonbonded pdb=" O ALA A 173 " pdb=" OG SER A 176 " model vdw 2.327 3.040 ... (remaining 61217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10.010 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.050 7614 Z= 0.438 Angle : 1.114 6.704 10388 Z= 0.785 Chirality : 0.062 0.221 1298 Planarity : 0.006 0.050 1274 Dihedral : 13.693 87.177 2506 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.70 % Allowed : 2.70 % Favored : 94.59 % 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: -2.32 (0.25), residues: 994 helix: -1.14 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -2.51 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 235 TYR 0.030 0.003 TYR A 451 PHE 0.014 0.002 PHE B 114 TRP 0.023 0.002 TRP A 193 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 7614) covalent geometry : angle 1.11447 (10388) hydrogen bonds : bond 0.18272 ( 604) hydrogen bonds : angle 7.80076 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.9065 (pt0) cc_final: 0.8822 (pp20) REVERT: A 75 ASN cc_start: 0.9669 (m-40) cc_final: 0.9458 (m-40) REVERT: A 185 PHE cc_start: 0.8481 (m-10) cc_final: 0.7487 (m-80) REVERT: A 188 CYS cc_start: 0.9343 (t) cc_final: 0.9063 (t) REVERT: A 234 ASP cc_start: 0.8992 (m-30) cc_final: 0.8774 (m-30) REVERT: A 264 MET cc_start: 0.8638 (mmp) cc_final: 0.8410 (mmp) REVERT: A 295 ARG cc_start: 0.8018 (ttt180) cc_final: 0.6983 (tmt170) REVERT: A 451 TYR cc_start: 0.7567 (t80) cc_final: 0.7347 (t80) REVERT: B 46 LEU cc_start: 0.9299 (mt) cc_final: 0.9013 (mt) REVERT: B 48 GLU cc_start: 0.9075 (pt0) cc_final: 0.8834 (pp20) REVERT: B 188 CYS cc_start: 0.9421 (t) cc_final: 0.9172 (t) REVERT: B 234 ASP cc_start: 0.9019 (m-30) cc_final: 0.8792 (m-30) REVERT: B 264 MET cc_start: 0.8710 (mmp) cc_final: 0.8400 (mmp) REVERT: B 295 ARG cc_start: 0.7964 (ttt180) cc_final: 0.6951 (tmt170) REVERT: B 451 TYR cc_start: 0.7727 (t80) cc_final: 0.7488 (t80) REVERT: B 521 MET cc_start: 0.8525 (pmm) cc_final: 0.8007 (pmm) outliers start: 20 outliers final: 3 residues processed: 204 average time/residue: 0.0605 time to fit residues: 18.4805 Evaluate side-chains 160 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0040 chunk 61 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 315 ASN A 654 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 315 ASN ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.111339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086091 restraints weight = 29189.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087961 restraints weight = 23328.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.089406 restraints weight = 19801.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.090687 restraints weight = 17480.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.091668 restraints weight = 15635.168| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7614 Z= 0.146 Angle : 0.653 7.224 10388 Z= 0.333 Chirality : 0.040 0.128 1298 Planarity : 0.005 0.056 1274 Dihedral : 4.732 20.866 1058 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.54 % Allowed : 2.97 % Favored : 96.49 % 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: -0.33 (0.26), residues: 994 helix: 0.17 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 295 TYR 0.010 0.001 TYR B 451 PHE 0.021 0.002 PHE A 114 TRP 0.018 0.002 TRP A 193 HIS 0.002 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7614) covalent geometry : angle 0.65336 (10388) hydrogen bonds : bond 0.04633 ( 604) hydrogen bonds : angle 5.25924 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9091 (mm) cc_final: 0.8878 (mm) REVERT: A 165 TYR cc_start: 0.9153 (m-10) cc_final: 0.8905 (m-80) REVERT: A 234 ASP cc_start: 0.9003 (m-30) cc_final: 0.8788 (m-30) REVERT: A 295 ARG cc_start: 0.8177 (ttt180) cc_final: 0.7171 (tmt170) REVERT: B 54 LEU cc_start: 0.9076 (mm) cc_final: 0.8868 (mm) REVERT: B 75 ASN cc_start: 0.9678 (m-40) cc_final: 0.9473 (m-40) REVERT: B 151 TYR cc_start: 0.8637 (t80) cc_final: 0.8068 (t80) REVERT: B 179 MET cc_start: 0.6089 (mmt) cc_final: 0.5877 (mmt) REVERT: B 188 CYS cc_start: 0.9298 (t) cc_final: 0.9038 (t) REVERT: B 234 ASP cc_start: 0.9089 (m-30) cc_final: 0.8853 (m-30) REVERT: B 264 MET cc_start: 0.8757 (mmp) cc_final: 0.8532 (mmp) REVERT: B 295 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7106 (tmt170) REVERT: B 521 MET cc_start: 0.8442 (pmm) cc_final: 0.8004 (pmm) outliers start: 4 outliers final: 0 residues processed: 189 average time/residue: 0.0586 time to fit residues: 16.7726 Evaluate side-chains 152 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.0570 chunk 77 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 654 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.112182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086831 restraints weight = 27921.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.088710 restraints weight = 22485.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.090457 restraints weight = 19166.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.091742 restraints weight = 16597.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.092686 restraints weight = 14789.773| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7614 Z= 0.127 Angle : 0.613 6.615 10388 Z= 0.307 Chirality : 0.039 0.131 1298 Planarity : 0.005 0.058 1274 Dihedral : 4.448 17.606 1058 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.27 % Allowed : 3.51 % Favored : 96.22 % 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: 0.49 (0.27), residues: 994 helix: 0.74 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 61 TYR 0.015 0.001 TYR A 168 PHE 0.018 0.001 PHE A 384 TRP 0.010 0.001 TRP A 679 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7614) covalent geometry : angle 0.61314 (10388) hydrogen bonds : bond 0.04121 ( 604) hydrogen bonds : angle 4.88602 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8936 (mm) cc_final: 0.8720 (mm) REVERT: A 75 ASN cc_start: 0.9557 (m-40) cc_final: 0.9316 (m-40) REVERT: A 85 LEU cc_start: 0.9547 (pp) cc_final: 0.9313 (pp) REVERT: A 185 PHE cc_start: 0.8442 (m-10) cc_final: 0.7500 (m-80) REVERT: A 234 ASP cc_start: 0.8788 (m-30) cc_final: 0.8580 (m-30) REVERT: A 264 MET cc_start: 0.8689 (mmp) cc_final: 0.8447 (mmp) REVERT: A 295 ARG cc_start: 0.8202 (ttt180) cc_final: 0.7207 (tmt170) REVERT: B 46 LEU cc_start: 0.9151 (mt) cc_final: 0.8926 (mt) REVERT: B 75 ASN cc_start: 0.9582 (m-40) cc_final: 0.9288 (m-40) REVERT: B 85 LEU cc_start: 0.9536 (pp) cc_final: 0.9283 (pp) REVERT: B 178 MET cc_start: 0.5407 (tmm) cc_final: 0.4889 (ppp) REVERT: B 234 ASP cc_start: 0.8863 (m-30) cc_final: 0.8634 (m-30) REVERT: B 264 MET cc_start: 0.8767 (mmp) cc_final: 0.8455 (mmp) REVERT: B 295 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7222 (tmt170) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.0613 time to fit residues: 16.4279 Evaluate side-chains 151 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 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 654 GLN A 683 GLN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.111342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.085781 restraints weight = 28626.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.087424 restraints weight = 23315.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088940 restraints weight = 20212.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.090046 restraints weight = 17895.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.091130 restraints weight = 16109.629| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7614 Z= 0.135 Angle : 0.606 6.678 10388 Z= 0.305 Chirality : 0.039 0.131 1298 Planarity : 0.005 0.062 1274 Dihedral : 4.262 16.429 1058 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.27 % Allowed : 3.11 % Favored : 96.62 % 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: 0.89 (0.27), residues: 994 helix: 1.05 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.21 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 61 TYR 0.018 0.001 TYR A 320 PHE 0.015 0.001 PHE A 114 TRP 0.008 0.001 TRP B 193 HIS 0.001 0.000 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7614) covalent geometry : angle 0.60611 (10388) hydrogen bonds : bond 0.04042 ( 604) hydrogen bonds : angle 4.73704 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9044 (mm) cc_final: 0.8826 (mm) REVERT: A 75 ASN cc_start: 0.9627 (m-40) cc_final: 0.9394 (m-40) REVERT: A 85 LEU cc_start: 0.9596 (pp) cc_final: 0.9356 (pp) REVERT: A 151 TYR cc_start: 0.8490 (t80) cc_final: 0.8085 (t80) REVERT: A 234 ASP cc_start: 0.8918 (m-30) cc_final: 0.8715 (m-30) REVERT: A 264 MET cc_start: 0.8763 (mmp) cc_final: 0.8505 (mmp) REVERT: A 295 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7368 (tmt170) REVERT: A 320 TYR cc_start: 0.8316 (m-80) cc_final: 0.7980 (m-80) REVERT: A 429 MET cc_start: 0.9239 (mmp) cc_final: 0.9038 (mmm) REVERT: B 85 LEU cc_start: 0.9580 (pp) cc_final: 0.9365 (pp) REVERT: B 151 TYR cc_start: 0.8572 (t80) cc_final: 0.8114 (t80) REVERT: B 179 MET cc_start: 0.6570 (tpp) cc_final: 0.5819 (tpp) REVERT: B 234 ASP cc_start: 0.8962 (m-30) cc_final: 0.8749 (m-30) REVERT: B 264 MET cc_start: 0.8862 (mmp) cc_final: 0.8575 (mmp) REVERT: B 295 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7435 (tmt170) REVERT: B 429 MET cc_start: 0.9137 (mmp) cc_final: 0.8919 (mmm) outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.0652 time to fit residues: 16.3779 Evaluate side-chains 147 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.110281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085621 restraints weight = 28436.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.087394 restraints weight = 23409.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.088794 restraints weight = 20048.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.089978 restraints weight = 17714.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.090760 restraints weight = 15973.764| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7614 Z= 0.137 Angle : 0.620 6.663 10388 Z= 0.308 Chirality : 0.039 0.135 1298 Planarity : 0.005 0.062 1274 Dihedral : 4.256 19.598 1058 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.27 % Allowed : 1.76 % Favored : 97.97 % 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: 0.93 (0.27), residues: 994 helix: 1.06 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.18 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.021 0.001 TYR A 458 PHE 0.019 0.001 PHE A 114 TRP 0.008 0.001 TRP B 193 HIS 0.000 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7614) covalent geometry : angle 0.61963 (10388) hydrogen bonds : bond 0.03956 ( 604) hydrogen bonds : angle 4.66373 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9605 (pp) cc_final: 0.9390 (pp) REVERT: A 234 ASP cc_start: 0.8828 (m-30) cc_final: 0.8616 (m-30) REVERT: A 264 MET cc_start: 0.8766 (mmp) cc_final: 0.8492 (mmp) REVERT: A 295 ARG cc_start: 0.8273 (ttt180) cc_final: 0.7342 (tmt170) REVERT: A 320 TYR cc_start: 0.8229 (m-80) cc_final: 0.7929 (m-80) REVERT: A 429 MET cc_start: 0.9238 (mmp) cc_final: 0.9035 (mmm) REVERT: A 521 MET cc_start: 0.8211 (pmm) cc_final: 0.8004 (pmm) REVERT: B 85 LEU cc_start: 0.9575 (pp) cc_final: 0.9368 (pp) REVERT: B 151 TYR cc_start: 0.8516 (t80) cc_final: 0.8103 (t80) REVERT: B 158 TYR cc_start: 0.8857 (m-80) cc_final: 0.8177 (m-80) REVERT: B 234 ASP cc_start: 0.8875 (m-30) cc_final: 0.8644 (m-30) REVERT: B 264 MET cc_start: 0.8870 (mmp) cc_final: 0.8557 (mmp) REVERT: B 295 ARG cc_start: 0.8262 (ttt180) cc_final: 0.7357 (tmt170) REVERT: B 338 MET cc_start: 0.8248 (ttt) cc_final: 0.8042 (ttt) REVERT: B 358 MET cc_start: 0.8985 (ptp) cc_final: 0.8740 (ptp) REVERT: B 429 MET cc_start: 0.9191 (mmp) cc_final: 0.8950 (mmm) outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.0651 time to fit residues: 16.4028 Evaluate side-chains 144 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 95 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087165 restraints weight = 28015.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.088977 restraints weight = 22808.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.090506 restraints weight = 19540.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.091788 restraints weight = 17056.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.092634 restraints weight = 15322.760| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7614 Z= 0.123 Angle : 0.600 6.865 10388 Z= 0.297 Chirality : 0.039 0.135 1298 Planarity : 0.005 0.063 1274 Dihedral : 4.148 18.561 1058 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.28), residues: 994 helix: 1.22 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.30 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.015 0.001 TYR B 158 PHE 0.017 0.001 PHE A 114 TRP 0.008 0.001 TRP B 193 HIS 0.000 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7614) covalent geometry : angle 0.59990 (10388) hydrogen bonds : bond 0.03865 ( 604) hydrogen bonds : angle 4.45583 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9607 (pp) cc_final: 0.9390 (pp) REVERT: A 234 ASP cc_start: 0.8819 (m-30) cc_final: 0.8615 (m-30) REVERT: A 264 MET cc_start: 0.8776 (mmp) cc_final: 0.8485 (mmp) REVERT: A 295 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7266 (tmt170) REVERT: A 320 TYR cc_start: 0.8182 (m-80) cc_final: 0.7964 (m-80) REVERT: A 429 MET cc_start: 0.9240 (mmp) cc_final: 0.9020 (mmm) REVERT: B 158 TYR cc_start: 0.8809 (m-80) cc_final: 0.8106 (m-80) REVERT: B 234 ASP cc_start: 0.8848 (m-30) cc_final: 0.8571 (m-30) REVERT: B 264 MET cc_start: 0.8834 (mmp) cc_final: 0.8528 (mmp) REVERT: B 295 ARG cc_start: 0.8243 (ttt180) cc_final: 0.7338 (tmt170) REVERT: B 358 MET cc_start: 0.8952 (ptp) cc_final: 0.8712 (ptp) REVERT: B 429 MET cc_start: 0.9212 (mmp) cc_final: 0.8938 (mmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0665 time to fit residues: 16.9086 Evaluate side-chains 149 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 81 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 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 654 GLN B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.087113 restraints weight = 28954.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.089068 restraints weight = 23677.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.090615 restraints weight = 20275.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.091743 restraints weight = 17860.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.092864 restraints weight = 16116.081| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7614 Z= 0.124 Angle : 0.609 6.776 10388 Z= 0.301 Chirality : 0.039 0.145 1298 Planarity : 0.005 0.063 1274 Dihedral : 4.059 16.543 1058 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.28), residues: 994 helix: 1.27 (0.19), residues: 814 sheet: None (None), residues: 0 loop : -1.40 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 235 TYR 0.013 0.001 TYR B 158 PHE 0.017 0.001 PHE B 102 TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7614) covalent geometry : angle 0.60860 (10388) hydrogen bonds : bond 0.03865 ( 604) hydrogen bonds : angle 4.38021 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9639 (pp) cc_final: 0.9433 (pp) REVERT: A 234 ASP cc_start: 0.8925 (m-30) cc_final: 0.8634 (m-30) REVERT: A 264 MET cc_start: 0.8792 (mmp) cc_final: 0.8483 (mmp) REVERT: A 295 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7223 (tmt170) REVERT: A 320 TYR cc_start: 0.8318 (m-80) cc_final: 0.8053 (m-80) REVERT: A 429 MET cc_start: 0.9264 (mmp) cc_final: 0.9043 (mmm) REVERT: B 85 LEU cc_start: 0.9558 (pp) cc_final: 0.9353 (pp) REVERT: B 102 PHE cc_start: 0.9104 (t80) cc_final: 0.8856 (t80) REVERT: B 158 TYR cc_start: 0.8909 (m-80) cc_final: 0.8185 (m-80) REVERT: B 234 ASP cc_start: 0.8868 (m-30) cc_final: 0.8417 (p0) REVERT: B 264 MET cc_start: 0.8856 (mmp) cc_final: 0.8532 (mmp) REVERT: B 295 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7281 (tmt170) REVERT: B 358 MET cc_start: 0.8986 (ptp) cc_final: 0.8666 (ptp) REVERT: B 384 PHE cc_start: 0.8632 (t80) cc_final: 0.8420 (t80) REVERT: B 429 MET cc_start: 0.9280 (mmp) cc_final: 0.8997 (mmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0647 time to fit residues: 16.2371 Evaluate side-chains 143 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.113033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.086826 restraints weight = 28676.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088756 restraints weight = 23473.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.090322 restraints weight = 20110.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.091280 restraints weight = 17735.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.092456 restraints weight = 16173.426| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7614 Z= 0.123 Angle : 0.628 8.442 10388 Z= 0.303 Chirality : 0.040 0.135 1298 Planarity : 0.005 0.063 1274 Dihedral : 4.038 16.807 1058 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.28), residues: 994 helix: 1.31 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 235 TYR 0.016 0.001 TYR B 359 PHE 0.020 0.001 PHE B 102 TRP 0.011 0.001 TRP B 489 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7614) covalent geometry : angle 0.62849 (10388) hydrogen bonds : bond 0.03804 ( 604) hydrogen bonds : angle 4.37516 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8873 (m-30) cc_final: 0.8388 (p0) REVERT: A 264 MET cc_start: 0.8781 (mmp) cc_final: 0.8481 (mmp) REVERT: A 295 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7204 (tmt170) REVERT: A 320 TYR cc_start: 0.8377 (m-80) cc_final: 0.8098 (m-80) REVERT: A 358 MET cc_start: 0.9017 (ptp) cc_final: 0.8696 (ptp) REVERT: A 429 MET cc_start: 0.9247 (mmp) cc_final: 0.9012 (mmm) REVERT: A 674 SER cc_start: 0.9340 (t) cc_final: 0.9131 (p) REVERT: B 102 PHE cc_start: 0.9103 (t80) cc_final: 0.8871 (t80) REVERT: B 158 TYR cc_start: 0.8886 (m-80) cc_final: 0.8179 (m-80) REVERT: B 234 ASP cc_start: 0.8900 (m-30) cc_final: 0.8438 (p0) REVERT: B 264 MET cc_start: 0.8854 (mmp) cc_final: 0.8537 (mmp) REVERT: B 295 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7114 (tmt170) REVERT: B 358 MET cc_start: 0.8987 (ptp) cc_final: 0.8656 (ptp) REVERT: B 384 PHE cc_start: 0.8576 (t80) cc_final: 0.8360 (t80) REVERT: B 429 MET cc_start: 0.9276 (mmp) cc_final: 0.8970 (mmm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0627 time to fit residues: 16.0010 Evaluate side-chains 138 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.113124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087756 restraints weight = 27914.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.089801 restraints weight = 22693.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.091159 restraints weight = 19234.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.092596 restraints weight = 17104.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093452 restraints weight = 15290.690| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7614 Z= 0.123 Angle : 0.628 7.330 10388 Z= 0.303 Chirality : 0.040 0.136 1298 Planarity : 0.005 0.064 1274 Dihedral : 3.977 16.813 1058 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 994 helix: 1.36 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.48 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 295 TYR 0.012 0.001 TYR B 158 PHE 0.022 0.001 PHE A 102 TRP 0.008 0.001 TRP B 193 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7614) covalent geometry : angle 0.62830 (10388) hydrogen bonds : bond 0.03800 ( 604) hydrogen bonds : angle 4.30195 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.315 Fit side-chains REVERT: A 234 ASP cc_start: 0.8847 (m-30) cc_final: 0.8375 (p0) REVERT: A 264 MET cc_start: 0.8769 (mmp) cc_final: 0.8468 (mmp) REVERT: A 295 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7128 (tmt170) REVERT: A 429 MET cc_start: 0.9232 (mmp) cc_final: 0.8999 (mmm) REVERT: A 674 SER cc_start: 0.9386 (t) cc_final: 0.9176 (p) REVERT: B 158 TYR cc_start: 0.8860 (m-80) cc_final: 0.8160 (m-80) REVERT: B 234 ASP cc_start: 0.8848 (m-30) cc_final: 0.8392 (p0) REVERT: B 264 MET cc_start: 0.8808 (mmp) cc_final: 0.8498 (mmp) REVERT: B 295 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7079 (tmt170) REVERT: B 358 MET cc_start: 0.9000 (ptp) cc_final: 0.8684 (ptp) REVERT: B 429 MET cc_start: 0.9262 (mmp) cc_final: 0.8932 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0646 time to fit residues: 16.1220 Evaluate side-chains 135 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 97 optimal weight: 0.0060 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 73 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.112260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.087654 restraints weight = 28254.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089688 restraints weight = 22737.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091108 restraints weight = 19086.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.092633 restraints weight = 16842.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.093742 restraints weight = 14857.572| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7614 Z= 0.119 Angle : 0.624 7.010 10388 Z= 0.299 Chirality : 0.040 0.133 1298 Planarity : 0.005 0.064 1274 Dihedral : 3.936 16.843 1058 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.28), residues: 994 helix: 1.46 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.50 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 295 TYR 0.016 0.001 TYR B 359 PHE 0.022 0.001 PHE A 102 TRP 0.008 0.001 TRP B 193 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7614) covalent geometry : angle 0.62432 (10388) hydrogen bonds : bond 0.03633 ( 604) hydrogen bonds : angle 4.24527 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 75 ASN cc_start: 0.9618 (m-40) cc_final: 0.9363 (m-40) REVERT: A 234 ASP cc_start: 0.8847 (m-30) cc_final: 0.8380 (p0) REVERT: A 264 MET cc_start: 0.8765 (mmp) cc_final: 0.8473 (mmp) REVERT: A 295 ARG cc_start: 0.7972 (ttt180) cc_final: 0.6973 (tmt170) REVERT: A 320 TYR cc_start: 0.8451 (m-80) cc_final: 0.8033 (m-80) REVERT: A 358 MET cc_start: 0.8951 (ptp) cc_final: 0.8633 (ptp) REVERT: A 674 SER cc_start: 0.9381 (t) cc_final: 0.9169 (p) REVERT: B 158 TYR cc_start: 0.8816 (m-80) cc_final: 0.8093 (m-80) REVERT: B 234 ASP cc_start: 0.8787 (m-30) cc_final: 0.8349 (p0) REVERT: B 264 MET cc_start: 0.8831 (mmp) cc_final: 0.8515 (mmp) REVERT: B 295 ARG cc_start: 0.7982 (ttt180) cc_final: 0.6977 (tmt170) REVERT: B 358 MET cc_start: 0.9009 (ptp) cc_final: 0.8648 (ptp) REVERT: B 429 MET cc_start: 0.9293 (mmp) cc_final: 0.8988 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0654 time to fit residues: 16.3518 Evaluate side-chains 137 residues out of total 894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.0050 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.109454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.087173 restraints weight = 28825.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.088607 restraints weight = 23832.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.089993 restraints weight = 20854.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.090876 restraints weight = 18478.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.091844 restraints weight = 16833.694| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7614 Z= 0.124 Angle : 0.632 7.538 10388 Z= 0.305 Chirality : 0.040 0.135 1298 Planarity : 0.005 0.063 1274 Dihedral : 3.891 17.429 1058 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.27), residues: 994 helix: 1.50 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.52 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 235 TYR 0.015 0.001 TYR B 320 PHE 0.020 0.001 PHE A 102 TRP 0.009 0.001 TRP B 193 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7614) covalent geometry : angle 0.63225 (10388) hydrogen bonds : bond 0.03716 ( 604) hydrogen bonds : angle 4.20972 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.89 seconds wall clock time: 28 minutes 6.70 seconds (1686.70 seconds total)