Starting phenix.real_space_refine on Wed Sep 17 03:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqs_60794/09_2025/9iqs_60794.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 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 26 5.16 5 C 1800 2.51 5 N 445 2.21 5 O 467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 2738 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2226 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Time building chain proxies: 0.83, per 1000 atoms: 0.30 Number of scatterers: 2738 At special positions: 0 Unit cell: (63.13, 70.62, 92.02, 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 26 16.00 O 467 8.00 N 445 7.00 C 1800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 24 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 42 " distance=2.04 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 429 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 66.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 666 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 69.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'B' and resid 28 through 61 removed outlier: 3.856A pdb=" N ARG B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 94 Processing helix chain 'B' and resid 103 through 136 removed outlier: 3.510A pdb=" N LEU B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 176 Proline residue: B 166 - end of helix removed outlier: 4.505A pdb=" N GLN B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 226 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 392 through 423 Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 457 Proline residue: B 450 - end of helix removed outlier: 3.914A pdb=" N ALA B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.768A pdb=" N ARG B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 42 removed outlier: 6.408A pdb=" N TYR A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 821 1.35 - 1.47: 735 1.47 - 1.59: 1217 1.59 - 1.71: 0 1.71 - 1.83: 35 Bond restraints: 2808 Sorted by residual: bond pdb=" C CYS A 46 " pdb=" N PRO A 47 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.75e+00 bond pdb=" CG LEU B 441 " pdb=" CD2 LEU B 441 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB GLU B 395 " pdb=" CG GLU B 395 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.16e-01 bond pdb=" CB ARG A 27 " pdb=" CG ARG A 27 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.68e-01 bond pdb=" CA THR A 60 " pdb=" C THR A 60 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.34e-02 5.57e+03 4.23e-01 ... (remaining 2803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 3771 2.16 - 4.32: 48 4.32 - 6.47: 14 6.47 - 8.63: 3 8.63 - 10.79: 1 Bond angle restraints: 3837 Sorted by residual: angle pdb=" CA LEU B 441 " pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " ideal model delta sigma weight residual 116.30 127.09 -10.79 3.50e+00 8.16e-02 9.50e+00 angle pdb=" CA MET B 211 " pdb=" CB MET B 211 " pdb=" CG MET B 211 " ideal model delta sigma weight residual 114.10 119.31 -5.21 2.00e+00 2.50e-01 6.78e+00 angle pdb=" C TRP B 440 " pdb=" N LEU B 441 " pdb=" CA LEU B 441 " ideal model delta sigma weight residual 121.94 117.11 4.83 2.00e+00 2.50e-01 5.83e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 124.48 -8.18 3.50e+00 8.16e-02 5.46e+00 angle pdb=" N LEU B 441 " pdb=" CA LEU B 441 " pdb=" CB LEU B 441 " ideal model delta sigma weight residual 110.42 114.07 -3.65 1.62e+00 3.81e-01 5.07e+00 ... (remaining 3832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 1509 17.92 - 35.85: 119 35.85 - 53.77: 21 53.77 - 71.69: 4 71.69 - 89.61: 4 Dihedral angle restraints: 1657 sinusoidal: 632 harmonic: 1025 Sorted by residual: dihedral pdb=" CB CYS B 426 " pdb=" SG CYS B 426 " pdb=" SG CYS B 429 " pdb=" CB CYS B 429 " ideal model delta sinusoidal sigma weight residual -86.00 -175.61 89.61 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 57 " pdb=" CB CYS A 57 " ideal model delta sinusoidal sigma weight residual 93.00 147.31 -54.31 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " pdb=" SG CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sinusoidal sigma weight residual -86.00 -57.25 -28.75 1 1.00e+01 1.00e-02 1.18e+01 ... (remaining 1654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 271 0.030 - 0.060: 118 0.060 - 0.091: 49 0.091 - 0.121: 22 0.121 - 0.151: 2 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA ILE A 32 " pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CB ILE A 32 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA VAL B 180 " pdb=" N VAL B 180 " pdb=" C VAL B 180 " pdb=" CB VAL B 180 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE B 187 " pdb=" N ILE B 187 " pdb=" C ILE B 187 " pdb=" CB ILE B 187 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 459 not shown) Planarity restraints: 462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 32 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 33 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 202 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ALA B 202 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA B 202 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA B 203 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 430 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 431 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " 0.022 5.00e-02 4.00e+02 ... (remaining 459 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 502 2.77 - 3.30: 2921 3.30 - 3.83: 4762 3.83 - 4.37: 5086 4.37 - 4.90: 8723 Nonbonded interactions: 21994 Sorted by model distance: nonbonded pdb=" ND1 HIS A 29 " pdb=" OD1 ASP A 53 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 2 " pdb=" O ASP A 61 " model vdw 2.240 3.040 nonbonded pdb=" O ILE B 410 " pdb=" OG1 THR B 414 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP B 78 " pdb=" OG SER B 446 " model vdw 2.250 3.040 nonbonded pdb=" O LEU B 421 " pdb=" OG1 THR B 424 " model vdw 2.296 3.040 ... (remaining 21989 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.060 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 0.042 2814 Z= 0.140 Angle : 0.708 10.787 3849 Z= 0.349 Chirality : 0.042 0.151 462 Planarity : 0.005 0.051 462 Dihedral : 13.517 79.650 973 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.47), residues: 339 helix: 1.94 (0.34), residues: 220 sheet: -1.96 (0.94), residues: 27 loop : -3.36 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 465 TYR 0.012 0.001 TYR B 113 PHE 0.015 0.001 PHE B 464 TRP 0.024 0.002 TRP B 171 HIS 0.001 0.000 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2808) covalent geometry : angle 0.70683 ( 3837) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.05576 ( 12) hydrogen bonds : bond 0.08460 ( 195) hydrogen bonds : angle 4.55086 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.103 Fit side-chains REVERT: B 32 MET cc_start: 0.7028 (tmm) cc_final: 0.6727 (tmm) REVERT: B 54 MET cc_start: 0.8000 (ptp) cc_final: 0.7709 (ptp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0583 time to fit residues: 4.3098 Evaluate side-chains 42 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.158394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.142172 restraints weight = 6678.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.144530 restraints weight = 4435.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146306 restraints weight = 3332.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.147317 restraints weight = 2683.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148433 restraints weight = 2322.384| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2814 Z= 0.171 Angle : 0.703 8.621 3849 Z= 0.358 Chirality : 0.043 0.154 462 Planarity : 0.005 0.045 462 Dihedral : 4.499 16.582 374 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.29 % Allowed : 11.18 % Favored : 85.53 % 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: 0.44 (0.47), residues: 339 helix: 2.04 (0.34), residues: 215 sheet: -2.14 (0.91), residues: 27 loop : -3.19 (0.61), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 27 TYR 0.015 0.002 TYR A 30 PHE 0.021 0.002 PHE B 464 TRP 0.018 0.001 TRP B 171 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 2808) covalent geometry : angle 0.69982 ( 3837) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.40261 ( 12) hydrogen bonds : bond 0.04593 ( 195) hydrogen bonds : angle 4.37383 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.070 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.0480 time to fit residues: 3.2774 Evaluate side-chains 49 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.159201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143217 restraints weight = 6736.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.145585 restraints weight = 4489.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.147334 restraints weight = 3377.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.148590 restraints weight = 2727.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.149257 restraints weight = 2325.944| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2814 Z= 0.145 Angle : 0.662 8.176 3849 Z= 0.334 Chirality : 0.042 0.130 462 Planarity : 0.005 0.042 462 Dihedral : 4.359 14.190 374 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.95 % Allowed : 15.46 % Favored : 80.59 % 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: 0.53 (0.47), residues: 339 helix: 2.11 (0.34), residues: 216 sheet: -2.11 (0.89), residues: 27 loop : -3.25 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.016 0.001 TYR A 30 PHE 0.016 0.001 PHE B 464 TRP 0.011 0.001 TRP B 171 HIS 0.016 0.003 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2808) covalent geometry : angle 0.65944 ( 3837) SS BOND : bond 0.00500 ( 6) SS BOND : angle 1.25698 ( 12) hydrogen bonds : bond 0.04425 ( 195) hydrogen bonds : angle 4.34461 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.106 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.0576 time to fit residues: 3.7499 Evaluate side-chains 51 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.155502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139483 restraints weight = 6620.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.141864 restraints weight = 4384.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.143683 restraints weight = 3296.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.144942 restraints weight = 2633.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.145910 restraints weight = 2219.393| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2814 Z= 0.196 Angle : 0.714 8.455 3849 Z= 0.364 Chirality : 0.043 0.133 462 Planarity : 0.005 0.043 462 Dihedral : 4.508 15.107 374 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.61 % Allowed : 15.13 % Favored : 80.26 % 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: 0.47 (0.47), residues: 339 helix: 1.98 (0.33), residues: 218 sheet: -2.18 (0.85), residues: 27 loop : -3.11 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.014 0.002 TYR B 97 PHE 0.019 0.002 PHE B 189 TRP 0.029 0.002 TRP B 171 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 2808) covalent geometry : angle 0.71105 ( 3837) SS BOND : bond 0.00519 ( 6) SS BOND : angle 1.38035 ( 12) hydrogen bonds : bond 0.04627 ( 195) hydrogen bonds : angle 4.40620 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.105 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.0474 time to fit residues: 3.1993 Evaluate side-chains 51 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.157600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.141985 restraints weight = 6575.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144515 restraints weight = 4289.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.146270 restraints weight = 3164.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147537 restraints weight = 2521.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148451 restraints weight = 2131.925| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2814 Z= 0.147 Angle : 0.679 8.048 3849 Z= 0.347 Chirality : 0.043 0.156 462 Planarity : 0.005 0.043 462 Dihedral : 4.456 14.166 374 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.59 % Allowed : 17.43 % Favored : 76.97 % 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: 0.55 (0.47), residues: 339 helix: 2.01 (0.34), residues: 218 sheet: -2.04 (0.84), residues: 27 loop : -3.03 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.017 0.002 TYR A 30 PHE 0.015 0.001 PHE B 464 TRP 0.021 0.001 TRP B 171 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2808) covalent geometry : angle 0.67583 ( 3837) SS BOND : bond 0.00489 ( 6) SS BOND : angle 1.30176 ( 12) hydrogen bonds : bond 0.04525 ( 195) hydrogen bonds : angle 4.32901 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.105 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 56 average time/residue: 0.0462 time to fit residues: 3.3011 Evaluate side-chains 56 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.157415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141443 restraints weight = 6607.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143997 restraints weight = 4289.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.145889 restraints weight = 3170.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146951 restraints weight = 2510.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.148041 restraints weight = 2139.616| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2814 Z= 0.154 Angle : 0.689 7.595 3849 Z= 0.349 Chirality : 0.044 0.197 462 Planarity : 0.005 0.041 462 Dihedral : 4.445 13.980 374 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.26 % Allowed : 18.09 % Favored : 76.64 % 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: 0.58 (0.47), residues: 339 helix: 1.95 (0.34), residues: 218 sheet: -1.48 (0.97), residues: 27 loop : -2.98 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.016 0.002 TYR A 30 PHE 0.015 0.001 PHE B 189 TRP 0.017 0.001 TRP B 171 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2808) covalent geometry : angle 0.68695 ( 3837) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.17081 ( 12) hydrogen bonds : bond 0.04490 ( 195) hydrogen bonds : angle 4.30661 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.105 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 52 average time/residue: 0.0449 time to fit residues: 3.0628 Evaluate side-chains 55 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.142721 restraints weight = 6600.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.145178 restraints weight = 4306.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146947 restraints weight = 3182.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.148156 restraints weight = 2542.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.149032 restraints weight = 2150.067| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2814 Z= 0.143 Angle : 0.680 8.325 3849 Z= 0.342 Chirality : 0.043 0.163 462 Planarity : 0.005 0.040 462 Dihedral : 4.356 14.369 374 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.92 % Allowed : 18.42 % Favored : 75.66 % 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: 0.71 (0.47), residues: 339 helix: 2.01 (0.34), residues: 219 sheet: -1.07 (1.04), residues: 27 loop : -3.00 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.016 0.001 TYR A 30 PHE 0.013 0.001 PHE B 189 TRP 0.018 0.001 TRP B 171 HIS 0.009 0.002 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2808) covalent geometry : angle 0.67860 ( 3837) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.09501 ( 12) hydrogen bonds : bond 0.04356 ( 195) hydrogen bonds : angle 4.28253 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.104 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 54 average time/residue: 0.0462 time to fit residues: 3.2375 Evaluate side-chains 54 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.157642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.142341 restraints weight = 6765.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144881 restraints weight = 4367.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.146709 restraints weight = 3195.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.147948 restraints weight = 2528.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.148668 restraints weight = 2119.760| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2814 Z= 0.146 Angle : 0.685 8.663 3849 Z= 0.344 Chirality : 0.043 0.158 462 Planarity : 0.005 0.040 462 Dihedral : 4.391 14.405 374 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.93 % Allowed : 19.74 % Favored : 75.33 % 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: 0.66 (0.47), residues: 339 helix: 1.79 (0.34), residues: 227 sheet: -0.68 (1.06), residues: 27 loop : -3.07 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 27 TYR 0.017 0.002 TYR B 92 PHE 0.013 0.001 PHE B 464 TRP 0.016 0.001 TRP B 171 HIS 0.007 0.002 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2808) covalent geometry : angle 0.68166 ( 3837) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.36053 ( 12) hydrogen bonds : bond 0.04396 ( 195) hydrogen bonds : angle 4.29401 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.0437 time to fit residues: 2.9266 Evaluate side-chains 54 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.158548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.143516 restraints weight = 6842.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.146060 restraints weight = 4338.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.147906 restraints weight = 3156.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.149157 restraints weight = 2488.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.150029 restraints weight = 2074.088| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2814 Z= 0.139 Angle : 0.681 8.918 3849 Z= 0.345 Chirality : 0.043 0.168 462 Planarity : 0.005 0.040 462 Dihedral : 4.293 14.741 374 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.93 % Allowed : 19.41 % Favored : 75.66 % 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: 0.75 (0.47), residues: 339 helix: 1.88 (0.34), residues: 225 sheet: -0.05 (1.13), residues: 25 loop : -3.17 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.016 0.001 TYR A 30 PHE 0.011 0.001 PHE B 464 TRP 0.018 0.001 TRP B 171 HIS 0.002 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2808) covalent geometry : angle 0.67855 ( 3837) SS BOND : bond 0.00389 ( 6) SS BOND : angle 1.23306 ( 12) hydrogen bonds : bond 0.04394 ( 195) hydrogen bonds : angle 4.29445 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 54 average time/residue: 0.0397 time to fit residues: 2.8057 Evaluate side-chains 51 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.156508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141464 restraints weight = 6710.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.144051 restraints weight = 4280.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.145822 restraints weight = 3121.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.147087 restraints weight = 2456.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.147965 restraints weight = 2052.066| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2814 Z= 0.171 Angle : 0.748 8.809 3849 Z= 0.376 Chirality : 0.045 0.167 462 Planarity : 0.005 0.040 462 Dihedral : 4.405 14.700 374 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.28 % Allowed : 21.05 % Favored : 74.67 % 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: 0.64 (0.47), residues: 339 helix: 1.72 (0.34), residues: 227 sheet: -0.37 (1.10), residues: 27 loop : -3.05 (0.63), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.016 0.002 TYR B 92 PHE 0.019 0.001 PHE B 189 TRP 0.046 0.002 TRP B 171 HIS 0.017 0.004 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2808) covalent geometry : angle 0.74519 ( 3837) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.31651 ( 12) hydrogen bonds : bond 0.04512 ( 195) hydrogen bonds : angle 4.46522 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.102 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 51 average time/residue: 0.0374 time to fit residues: 2.4835 Evaluate side-chains 53 residues out of total 304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.156307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.141263 restraints weight = 6696.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.143821 restraints weight = 4322.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.145589 restraints weight = 3168.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.146941 restraints weight = 2510.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.147834 restraints weight = 2086.374| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2814 Z= 0.171 Angle : 0.756 9.190 3849 Z= 0.384 Chirality : 0.045 0.198 462 Planarity : 0.005 0.040 462 Dihedral : 4.432 14.902 374 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.95 % Allowed : 22.04 % Favored : 74.01 % 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: 0.57 (0.47), residues: 339 helix: 1.63 (0.34), residues: 227 sheet: 0.15 (1.13), residues: 25 loop : -3.10 (0.62), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.014 0.001 TYR A 30 PHE 0.019 0.001 PHE B 189 TRP 0.039 0.002 TRP B 171 HIS 0.006 0.002 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2808) covalent geometry : angle 0.75315 ( 3837) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.33002 ( 12) hydrogen bonds : bond 0.04589 ( 195) hydrogen bonds : angle 4.54446 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 680.07 seconds wall clock time: 12 minutes 28.62 seconds (748.62 seconds total)