Starting phenix.real_space_refine on Wed Sep 17 03:13:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.map" model { file = "/net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boj_44744/09_2025/9boj_44744.cif" } resolution = 3.5 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= 0.041 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 14 5.16 5 C 1728 2.51 5 N 401 2.21 5 O 417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2560 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2560 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 316} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 0.77, per 1000 atoms: 0.30 Number of scatterers: 2560 At special positions: 0 Unit cell: (73.425, 58.575, 75.9, 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 14 16.00 O 417 8.00 N 401 7.00 C 1728 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: 0.15 Conformation dependent library (CDL) restraints added in 65.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 84.7% alpha, 0.0% 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 111 through 131 removed outlier: 4.112A pdb=" N ILE B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.836A pdb=" N VAL B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 283 removed outlier: 8.089A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 313 Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 332 through 360 Processing helix chain 'B' and resid 368 through 419 removed outlier: 3.835A pdb=" N ILE B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 441 Processing helix chain 'B' and resid 453 through 478 Processing helix chain 'B' and resid 487 through 513 removed outlier: 3.638A pdb=" N ALA B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 648 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: 0.37 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 747 1.34 - 1.46: 781 1.46 - 1.58: 1095 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2644 Sorted by residual: bond pdb=" N TRP B 166 " pdb=" CA TRP B 166 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.90e-02 2.77e+03 1.18e+00 bond pdb=" N ASP B 363 " pdb=" CA ASP B 363 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.28e-01 bond pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.69e-02 3.50e+03 7.11e-01 bond pdb=" CA ASP B 363 " pdb=" C ASP B 363 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.34e-02 5.57e+03 3.17e-01 bond pdb=" CB TRP B 378 " pdb=" CG TRP B 378 " ideal model delta sigma weight residual 1.498 1.515 -0.017 3.10e-02 1.04e+03 2.86e-01 ... (remaining 2639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 3552 1.60 - 3.20: 51 3.20 - 4.80: 10 4.80 - 6.40: 2 6.40 - 8.00: 2 Bond angle restraints: 3617 Sorted by residual: angle pdb=" CA TRP B 166 " pdb=" CB TRP B 166 " pdb=" CG TRP B 166 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" N TRP B 166 " pdb=" CA TRP B 166 " pdb=" CB TRP B 166 " ideal model delta sigma weight residual 110.50 116.89 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CA TRP B 378 " pdb=" CB TRP B 378 " pdb=" CG TRP B 378 " ideal model delta sigma weight residual 113.60 120.16 -6.56 1.90e+00 2.77e-01 1.19e+01 angle pdb=" CA TRP B 166 " pdb=" C TRP B 166 " pdb=" O TRP B 166 " ideal model delta sigma weight residual 120.80 116.98 3.82 1.70e+00 3.46e-01 5.06e+00 angle pdb=" C ASP B 363 " pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " ideal model delta sigma weight residual 110.42 114.84 -4.42 1.99e+00 2.53e-01 4.93e+00 ... (remaining 3612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 1324 16.49 - 32.98: 92 32.98 - 49.47: 30 49.47 - 65.96: 7 65.96 - 82.45: 2 Dihedral angle restraints: 1455 sinusoidal: 504 harmonic: 951 Sorted by residual: dihedral pdb=" N GLN B 160 " pdb=" CA GLN B 160 " pdb=" CB GLN B 160 " pdb=" CG GLN B 160 " ideal model delta sinusoidal sigma weight residual -180.00 -120.18 -59.82 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET B 295 " pdb=" CA MET B 295 " pdb=" CB MET B 295 " pdb=" CG MET B 295 " ideal model delta sinusoidal sigma weight residual 180.00 120.68 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB GLU B 298 " pdb=" CG GLU B 298 " pdb=" CD GLU B 298 " pdb=" OE1 GLU B 298 " ideal model delta sinusoidal sigma weight residual 0.00 -82.45 82.45 1 3.00e+01 1.11e-03 9.26e+00 ... (remaining 1452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 254 0.028 - 0.056: 119 0.056 - 0.084: 31 0.084 - 0.112: 7 0.112 - 0.140: 1 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA TRP B 166 " pdb=" N TRP B 166 " pdb=" C TRP B 166 " pdb=" CB TRP B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 483 " pdb=" N ILE B 483 " pdb=" C ILE B 483 " pdb=" CB ILE B 483 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.03e-01 chirality pdb=" CA PHE B 311 " pdb=" N PHE B 311 " pdb=" C PHE B 311 " pdb=" CB PHE B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 409 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 165 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C ARG B 165 " 0.071 2.00e-02 2.50e+03 pdb=" O ARG B 165 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP B 166 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 166 " 0.016 2.00e-02 2.50e+03 1.40e-02 4.93e+00 pdb=" CG TRP B 166 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 166 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 166 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 166 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 166 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 166 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 166 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 261 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ILE B 261 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE B 261 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 262 " 0.012 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 895 2.85 - 3.36: 2680 3.36 - 3.87: 4274 3.87 - 4.39: 4450 4.39 - 4.90: 8049 Nonbonded interactions: 20348 Sorted by model distance: nonbonded pdb=" O TYR B 441 " pdb=" OH TYR B 460 " model vdw 2.333 3.040 nonbonded pdb=" O ARG B 452 " pdb=" NH2 ARG B 456 " model vdw 2.364 3.120 nonbonded pdb=" O ASP B 135 " pdb=" N GLN B 141 " model vdw 2.376 3.120 nonbonded pdb=" O ARG B 386 " pdb=" OG1 THR B 389 " model vdw 2.537 3.040 nonbonded pdb=" O ARG B 106 " pdb=" OH TYR B 292 " model vdw 2.541 3.040 ... (remaining 20343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 0.021 2644 Z= 0.137 Angle : 0.531 8.001 3617 Z= 0.300 Chirality : 0.034 0.140 412 Planarity : 0.004 0.041 430 Dihedral : 13.584 82.449 837 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 8.70 % Allowed : 7.91 % Favored : 83.40 % 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: 1.83 (0.48), residues: 315 helix: 2.00 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.57 (0.81), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 358 TYR 0.013 0.001 TYR B 297 PHE 0.010 0.001 PHE B 380 TRP 0.036 0.002 TRP B 166 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2644) covalent geometry : angle 0.53078 ( 3617) hydrogen bonds : bond 0.08642 ( 218) hydrogen bonds : angle 4.43576 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.075 Fit side-chains REVERT: B 361 ARG cc_start: 0.6125 (tpp80) cc_final: 0.3801 (ptm-80) REVERT: B 369 TYR cc_start: 0.7269 (m-80) cc_final: 0.6968 (m-80) REVERT: B 370 MET cc_start: 0.6007 (mtm) cc_final: 0.5716 (mmt) REVERT: B 457 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 492 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7248 (mp) outliers start: 22 outliers final: 6 residues processed: 92 average time/residue: 0.0659 time to fit residues: 7.0269 Evaluate side-chains 58 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.163273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148859 restraints weight = 3697.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152364 restraints weight = 1964.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154601 restraints weight = 1270.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.156071 restraints weight = 920.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.156958 restraints weight = 722.525| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2644 Z= 0.175 Angle : 0.594 7.148 3617 Z= 0.307 Chirality : 0.038 0.172 412 Planarity : 0.003 0.030 430 Dihedral : 7.496 46.816 358 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.11 % Allowed : 13.44 % Favored : 79.45 % 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: 1.61 (0.48), residues: 315 helix: 1.79 (0.31), residues: 269 sheet: None (None), residues: 0 loop : -3.48 (0.78), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.016 0.002 TYR B 297 PHE 0.014 0.002 PHE B 393 TRP 0.025 0.002 TRP B 378 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2644) covalent geometry : angle 0.59362 ( 3617) hydrogen bonds : bond 0.04292 ( 218) hydrogen bonds : angle 4.20467 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.054 Fit side-chains REVERT: B 129 ASP cc_start: 0.7973 (m-30) cc_final: 0.7710 (m-30) REVERT: B 295 MET cc_start: 0.6758 (tmm) cc_final: 0.6443 (tmm) REVERT: B 361 ARG cc_start: 0.5620 (tpp80) cc_final: 0.3591 (ptm-80) REVERT: B 369 TYR cc_start: 0.7367 (m-80) cc_final: 0.7051 (m-80) REVERT: B 454 ARG cc_start: 0.7571 (ttm110) cc_final: 0.6170 (mmt180) outliers start: 18 outliers final: 8 residues processed: 68 average time/residue: 0.0476 time to fit residues: 3.8579 Evaluate side-chains 53 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.147020 restraints weight = 3740.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150308 restraints weight = 2076.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152265 restraints weight = 1380.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153800 restraints weight = 1051.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154967 restraints weight = 852.420| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2644 Z= 0.126 Angle : 0.536 7.841 3617 Z= 0.276 Chirality : 0.037 0.283 412 Planarity : 0.003 0.029 430 Dihedral : 6.008 47.539 349 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.93 % Allowed : 17.00 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.48), residues: 315 helix: 1.84 (0.31), residues: 270 sheet: None (None), residues: 0 loop : -3.73 (0.72), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 456 TYR 0.012 0.001 TYR B 297 PHE 0.028 0.001 PHE B 393 TRP 0.020 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2644) covalent geometry : angle 0.53592 ( 3617) hydrogen bonds : bond 0.03977 ( 218) hydrogen bonds : angle 4.02191 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.106 Fit side-chains REVERT: B 129 ASP cc_start: 0.8009 (m-30) cc_final: 0.7739 (m-30) REVERT: B 281 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7227 (ptm160) REVERT: B 295 MET cc_start: 0.6814 (tmm) cc_final: 0.6559 (tmm) REVERT: B 361 ARG cc_start: 0.5464 (tpp80) cc_final: 0.3480 (ptm-80) REVERT: B 369 TYR cc_start: 0.7221 (m-80) cc_final: 0.6976 (m-80) REVERT: B 448 VAL cc_start: 0.5821 (OUTLIER) cc_final: 0.5092 (t) REVERT: B 454 ARG cc_start: 0.7544 (ttm110) cc_final: 0.6093 (mmt180) REVERT: B 492 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6738 (mp) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.0758 time to fit residues: 5.5711 Evaluate side-chains 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144786 restraints weight = 3742.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147404 restraints weight = 2158.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149495 restraints weight = 1515.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150999 restraints weight = 1168.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151543 restraints weight = 934.553| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2644 Z= 0.149 Angle : 0.557 7.134 3617 Z= 0.291 Chirality : 0.038 0.272 412 Planarity : 0.003 0.028 430 Dihedral : 6.083 47.446 349 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.35 % Allowed : 18.58 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.47), residues: 315 helix: 1.75 (0.31), residues: 270 sheet: None (None), residues: 0 loop : -3.85 (0.71), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.015 0.001 TYR B 297 PHE 0.013 0.001 PHE B 380 TRP 0.025 0.002 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2644) covalent geometry : angle 0.55695 ( 3617) hydrogen bonds : bond 0.04119 ( 218) hydrogen bonds : angle 4.05456 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.110 Fit side-chains REVERT: B 129 ASP cc_start: 0.7966 (m-30) cc_final: 0.7687 (m-30) REVERT: B 295 MET cc_start: 0.6813 (tmm) cc_final: 0.6548 (tmm) REVERT: B 361 ARG cc_start: 0.5469 (tpp80) cc_final: 0.3506 (ptm-80) REVERT: B 369 TYR cc_start: 0.7249 (m-80) cc_final: 0.6865 (m-80) REVERT: B 454 ARG cc_start: 0.7423 (ttm110) cc_final: 0.6120 (mmt180) REVERT: B 492 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6934 (mp) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.0725 time to fit residues: 4.9347 Evaluate side-chains 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145058 restraints weight = 3720.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147902 restraints weight = 2208.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149861 restraints weight = 1539.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151051 restraints weight = 1195.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152034 restraints weight = 1000.510| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2644 Z= 0.131 Angle : 0.527 6.396 3617 Z= 0.277 Chirality : 0.036 0.186 412 Planarity : 0.003 0.028 430 Dihedral : 5.954 50.346 349 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.53 % Allowed : 17.79 % Favored : 76.68 % 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: 1.75 (0.48), residues: 315 helix: 1.86 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.02 (0.83), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 456 TYR 0.014 0.001 TYR B 297 PHE 0.024 0.001 PHE B 150 TRP 0.022 0.002 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2644) covalent geometry : angle 0.52701 ( 3617) hydrogen bonds : bond 0.03911 ( 218) hydrogen bonds : angle 3.99084 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.082 Fit side-chains REVERT: B 129 ASP cc_start: 0.7898 (m-30) cc_final: 0.7621 (m-30) REVERT: B 295 MET cc_start: 0.6802 (tmm) cc_final: 0.6534 (tmm) REVERT: B 361 ARG cc_start: 0.5473 (tpp80) cc_final: 0.3571 (ptm-80) REVERT: B 369 TYR cc_start: 0.7153 (m-80) cc_final: 0.6930 (m-80) REVERT: B 454 ARG cc_start: 0.7325 (ttm110) cc_final: 0.6124 (mmt180) REVERT: B 466 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7047 (tp) REVERT: B 492 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7000 (mp) outliers start: 14 outliers final: 11 residues processed: 61 average time/residue: 0.0594 time to fit residues: 4.2608 Evaluate side-chains 64 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145938 restraints weight = 3680.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148758 restraints weight = 2147.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150613 restraints weight = 1500.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152056 restraints weight = 1163.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152855 restraints weight = 951.467| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2644 Z= 0.123 Angle : 0.547 7.626 3617 Z= 0.280 Chirality : 0.036 0.209 412 Planarity : 0.003 0.027 430 Dihedral : 5.871 49.805 349 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.53 % Allowed : 15.81 % Favored : 78.66 % 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: 1.74 (0.48), residues: 315 helix: 1.86 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.15 (0.85), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.012 0.001 TYR B 297 PHE 0.011 0.001 PHE B 393 TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2644) covalent geometry : angle 0.54729 ( 3617) hydrogen bonds : bond 0.03852 ( 218) hydrogen bonds : angle 3.99158 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.099 Fit side-chains REVERT: B 115 ILE cc_start: 0.5894 (mp) cc_final: 0.5603 (mt) REVERT: B 129 ASP cc_start: 0.7787 (m-30) cc_final: 0.7546 (m-30) REVERT: B 295 MET cc_start: 0.6786 (tmm) cc_final: 0.6520 (tmm) REVERT: B 361 ARG cc_start: 0.5439 (tpp80) cc_final: 0.3588 (ptm-80) REVERT: B 369 TYR cc_start: 0.7158 (m-80) cc_final: 0.6499 (m-80) REVERT: B 454 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6127 (mmt180) REVERT: B 492 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6991 (mp) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.0711 time to fit residues: 5.2916 Evaluate side-chains 62 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144134 restraints weight = 3756.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146460 restraints weight = 2245.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148604 restraints weight = 1630.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150041 restraints weight = 1268.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150801 restraints weight = 1041.854| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2644 Z= 0.141 Angle : 0.579 8.771 3617 Z= 0.294 Chirality : 0.037 0.186 412 Planarity : 0.003 0.027 430 Dihedral : 5.583 51.664 347 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.53 % Allowed : 17.39 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.48), residues: 315 helix: 1.78 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.27 (0.82), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.015 0.001 TYR B 297 PHE 0.024 0.001 PHE B 150 TRP 0.024 0.002 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2644) covalent geometry : angle 0.57874 ( 3617) hydrogen bonds : bond 0.03982 ( 218) hydrogen bonds : angle 4.03565 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.096 Fit side-chains REVERT: B 115 ILE cc_start: 0.5843 (mp) cc_final: 0.5570 (mt) REVERT: B 129 ASP cc_start: 0.7787 (m-30) cc_final: 0.7546 (m-30) REVERT: B 144 TRP cc_start: 0.7560 (m-10) cc_final: 0.7275 (m-10) REVERT: B 361 ARG cc_start: 0.5438 (tpp80) cc_final: 0.3532 (ptm-80) REVERT: B 369 TYR cc_start: 0.7168 (m-80) cc_final: 0.6507 (m-80) REVERT: B 454 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6137 (mmt180) REVERT: B 492 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6936 (mp) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.0726 time to fit residues: 5.2931 Evaluate side-chains 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145789 restraints weight = 3754.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148743 restraints weight = 2135.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150826 restraints weight = 1465.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152271 restraints weight = 1111.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153228 restraints weight = 899.347| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2644 Z= 0.128 Angle : 0.570 9.342 3617 Z= 0.288 Chirality : 0.036 0.128 412 Planarity : 0.003 0.027 430 Dihedral : 5.495 51.172 347 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.53 % Allowed : 17.00 % Favored : 77.47 % 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: 1.65 (0.48), residues: 315 helix: 1.82 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.35 (0.81), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 456 TYR 0.013 0.001 TYR B 297 PHE 0.024 0.001 PHE B 150 TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2644) covalent geometry : angle 0.56967 ( 3617) hydrogen bonds : bond 0.03945 ( 218) hydrogen bonds : angle 4.00185 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.093 Fit side-chains REVERT: B 115 ILE cc_start: 0.5803 (mp) cc_final: 0.5535 (mt) REVERT: B 129 ASP cc_start: 0.7806 (m-30) cc_final: 0.7549 (m-30) REVERT: B 144 TRP cc_start: 0.7592 (m-10) cc_final: 0.7302 (m-10) REVERT: B 361 ARG cc_start: 0.5392 (OUTLIER) cc_final: 0.3498 (ptm-80) REVERT: B 369 TYR cc_start: 0.7025 (m-80) cc_final: 0.6469 (m-80) REVERT: B 454 ARG cc_start: 0.7357 (ttm110) cc_final: 0.6077 (mmt180) REVERT: B 492 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6842 (mp) outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.0705 time to fit residues: 5.4974 Evaluate side-chains 67 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145659 restraints weight = 3743.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148391 restraints weight = 2216.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150281 restraints weight = 1555.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151819 restraints weight = 1205.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152876 restraints weight = 970.124| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2644 Z= 0.133 Angle : 0.584 9.732 3617 Z= 0.297 Chirality : 0.041 0.283 412 Planarity : 0.003 0.027 430 Dihedral : 5.497 51.545 347 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.93 % Allowed : 18.58 % Favored : 75.49 % 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: 1.70 (0.48), residues: 315 helix: 1.87 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.41 (0.79), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 456 TYR 0.013 0.001 TYR B 297 PHE 0.023 0.001 PHE B 150 TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 2644) covalent geometry : angle 0.58392 ( 3617) hydrogen bonds : bond 0.03974 ( 218) hydrogen bonds : angle 4.01518 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.092 Fit side-chains REVERT: B 115 ILE cc_start: 0.5726 (mp) cc_final: 0.5452 (mt) REVERT: B 129 ASP cc_start: 0.7759 (m-30) cc_final: 0.7523 (m-30) REVERT: B 144 TRP cc_start: 0.7554 (m-10) cc_final: 0.7309 (m-10) REVERT: B 166 TRP cc_start: 0.6955 (p90) cc_final: 0.5609 (t-100) REVERT: B 361 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.3586 (ptm-80) REVERT: B 369 TYR cc_start: 0.7036 (m-80) cc_final: 0.6513 (m-80) REVERT: B 398 GLN cc_start: 0.6568 (pm20) cc_final: 0.6074 (pm20) REVERT: B 454 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6110 (mmt180) REVERT: B 492 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6908 (mp) outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.0672 time to fit residues: 5.1976 Evaluate side-chains 68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.160642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145668 restraints weight = 3725.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148678 restraints weight = 2127.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150462 restraints weight = 1447.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151976 restraints weight = 1127.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152786 restraints weight = 912.496| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2644 Z= 0.140 Angle : 0.614 10.139 3617 Z= 0.306 Chirality : 0.040 0.240 412 Planarity : 0.003 0.027 430 Dihedral : 5.556 51.507 347 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.93 % Allowed : 18.58 % Favored : 75.49 % 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: 1.63 (0.48), residues: 315 helix: 1.82 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.42 (0.78), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 456 TYR 0.014 0.001 TYR B 297 PHE 0.024 0.001 PHE B 150 TRP 0.023 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2644) covalent geometry : angle 0.61416 ( 3617) hydrogen bonds : bond 0.04045 ( 218) hydrogen bonds : angle 4.06947 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.100 Fit side-chains REVERT: B 115 ILE cc_start: 0.5760 (mp) cc_final: 0.5505 (mt) REVERT: B 129 ASP cc_start: 0.7787 (m-30) cc_final: 0.7553 (m-30) REVERT: B 144 TRP cc_start: 0.7594 (m-10) cc_final: 0.7302 (m-10) REVERT: B 166 TRP cc_start: 0.6959 (p90) cc_final: 0.5589 (t-100) REVERT: B 361 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.3522 (ptm-80) REVERT: B 369 TYR cc_start: 0.7052 (m-80) cc_final: 0.6497 (m-80) REVERT: B 398 GLN cc_start: 0.6673 (pm20) cc_final: 0.6248 (pm20) REVERT: B 454 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6091 (mmt180) REVERT: B 492 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6866 (mp) REVERT: B 512 PHE cc_start: 0.4374 (t80) cc_final: 0.4092 (t80) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.0771 time to fit residues: 5.8132 Evaluate side-chains 66 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146937 restraints weight = 3746.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149510 restraints weight = 2181.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151690 restraints weight = 1544.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152790 restraints weight = 1172.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153761 restraints weight = 978.223| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2644 Z= 0.125 Angle : 0.617 12.850 3617 Z= 0.301 Chirality : 0.042 0.271 412 Planarity : 0.003 0.027 430 Dihedral : 5.469 51.277 347 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.74 % Allowed : 20.55 % Favored : 74.70 % 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: 1.75 (0.48), residues: 315 helix: 1.91 (0.32), residues: 268 sheet: None (None), residues: 0 loop : -3.46 (0.77), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 456 TYR 0.013 0.001 TYR B 461 PHE 0.024 0.001 PHE B 150 TRP 0.020 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2644) covalent geometry : angle 0.61654 ( 3617) hydrogen bonds : bond 0.03938 ( 218) hydrogen bonds : angle 4.02437 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 654.60 seconds wall clock time: 11 minutes 58.28 seconds (718.28 seconds total)