Starting phenix.real_space_refine on Fri Aug 22 14:12:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.map" model { file = "/net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xon_33353/08_2025/7xon_33353.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 1.28, per 1000 atoms: 0.33 Number of scatterers: 3855 At special positions: 0 Unit cell: (71.34, 74.82, 85.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 773 8.00 N 665 7.00 C 2397 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: 0.32 Conformation dependent library (CDL) restraints added in 166.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 59.9% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.509A pdb=" N ARG B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.781A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 110 removed outlier: 3.562A pdb=" N ALA B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.700A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 243 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.689A pdb=" N ALA B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.914A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.623A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 459 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.591A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 479 267 hydrogen bonds defined for protein. 765 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: 0.65 Time building geometry restraints manager: 0.44 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: 1341 1.34 - 1.46: 643 1.46 - 1.58: 1862 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CB LYS B 242 " pdb=" CG LYS B 242 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.25e-01 bond pdb=" CG LYS B 242 " pdb=" CD LYS B 242 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.97e-01 bond pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 1.520 1.529 -0.008 1.23e-02 6.61e+03 4.72e-01 bond pdb=" CB LYS B 142 " pdb=" CG LYS B 142 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.06e-01 bond pdb=" CA GLU B 61 " pdb=" C GLU B 61 " ideal model delta sigma weight residual 1.523 1.529 -0.007 1.10e-02 8.26e+03 3.56e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 5117 1.20 - 2.41: 88 2.41 - 3.61: 32 3.61 - 4.82: 3 4.82 - 6.02: 3 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLY B 9 " pdb=" CA GLY B 9 " pdb=" C GLY B 9 " ideal model delta sigma weight residual 111.24 116.45 -5.21 1.49e+00 4.50e-01 1.22e+01 angle pdb=" N ILE B 230 " pdb=" CA ILE B 230 " pdb=" C ILE B 230 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CB LYS B 242 " pdb=" CG LYS B 242 " pdb=" CD LYS B 242 " ideal model delta sigma weight residual 111.30 117.32 -6.02 2.30e+00 1.89e-01 6.85e+00 angle pdb=" CA LYS B 142 " pdb=" CB LYS B 142 " pdb=" CG LYS B 142 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA ILE B 230 " pdb=" C ILE B 230 " pdb=" N ARG B 231 " ideal model delta sigma weight residual 118.65 116.61 2.04 1.07e+00 8.73e-01 3.62e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2240 17.17 - 34.34: 136 34.34 - 51.51: 25 51.51 - 68.68: 5 68.68 - 85.85: 6 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA MET B 166 " pdb=" C MET B 166 " pdb=" N ASP B 167 " pdb=" CA ASP B 167 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " pdb=" OD1 ASP B 428 " ideal model delta sinusoidal sigma weight residual -30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA LYS B 245 " pdb=" CB LYS B 245 " pdb=" CG LYS B 245 " pdb=" CD LYS B 245 " ideal model delta sinusoidal sigma weight residual -180.00 -126.14 -53.86 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 370 0.024 - 0.047: 143 0.047 - 0.071: 66 0.071 - 0.095: 33 0.095 - 0.118: 26 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL B 213 " pdb=" N VAL B 213 " pdb=" C VAL B 213 " pdb=" CB VAL B 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 332 " pdb=" N ILE B 332 " pdb=" C ILE B 332 " pdb=" CB ILE B 332 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 245 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.15e-01 pdb=" N PRO B 246 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 461 " 0.013 5.00e-02 4.00e+02 1.92e-02 5.88e-01 pdb=" N PRO B 462 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 46 " -0.010 5.00e-02 4.00e+02 1.57e-02 3.96e-01 pdb=" N PRO B 47 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.009 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1202 2.84 - 3.35: 4019 3.35 - 3.87: 6388 3.87 - 4.38: 6838 4.38 - 4.90: 12153 Nonbonded interactions: 30600 Sorted by model distance: nonbonded pdb=" NH1 ARG B 421 " pdb=" O VAL B 469 " model vdw 2.325 3.120 nonbonded pdb=" O GLU B 339 " pdb=" NE2 GLN B 343 " model vdw 2.333 3.120 nonbonded pdb=" O SER B 463 " pdb=" ND2 ASN B 467 " model vdw 2.363 3.120 nonbonded pdb=" OD1 ASN B 229 " pdb=" N ILE B 230 " model vdw 2.377 3.120 nonbonded pdb=" NH2 ARG B 421 " pdb=" O TYR B 476 " model vdw 2.386 3.120 ... (remaining 30595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.080 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.002 0.027 3883 Z= 0.110 Angle : 0.467 6.021 5243 Z= 0.257 Chirality : 0.039 0.118 638 Planarity : 0.002 0.023 687 Dihedral : 12.444 85.845 1464 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 2.61 (0.37), residues: 522 helix: 2.76 (0.30), residues: 290 sheet: 0.99 (0.61), residues: 74 loop : 0.16 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.007 0.001 TYR B 199 PHE 0.007 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3883) covalent geometry : angle 0.46708 ( 5243) hydrogen bonds : bond 0.14705 ( 267) hydrogen bonds : angle 5.00611 ( 765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: B 52 ASP cc_start: 0.8163 (t70) cc_final: 0.7961 (t0) REVERT: B 73 MET cc_start: 0.8729 (ptp) cc_final: 0.8454 (ptm) REVERT: B 121 ASP cc_start: 0.8773 (m-30) cc_final: 0.8464 (m-30) REVERT: B 254 VAL cc_start: 0.9521 (t) cc_final: 0.9133 (t) REVERT: B 307 MET cc_start: 0.8529 (mpp) cc_final: 0.8222 (mpp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0686 time to fit residues: 3.2984 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049096 restraints weight = 13152.344| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.45 r_work: 0.2780 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3883 Z= 0.215 Angle : 0.543 6.164 5243 Z= 0.290 Chirality : 0.042 0.139 638 Planarity : 0.003 0.019 687 Dihedral : 3.757 17.373 552 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 6.68 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.36), residues: 522 helix: 2.63 (0.29), residues: 299 sheet: 0.89 (0.59), residues: 74 loop : -0.11 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 421 TYR 0.008 0.001 TYR B 506 PHE 0.007 0.001 PHE B 66 HIS 0.001 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3883) covalent geometry : angle 0.54347 ( 5243) hydrogen bonds : bond 0.04695 ( 267) hydrogen bonds : angle 4.27792 ( 765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.162 Fit side-chains REVERT: B 193 MET cc_start: 0.9148 (ttm) cc_final: 0.8900 (ttm) REVERT: B 307 MET cc_start: 0.8714 (mpp) cc_final: 0.8365 (mpp) REVERT: B 338 GLU cc_start: 0.8449 (tp30) cc_final: 0.8223 (tp30) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.0517 time to fit residues: 2.1124 Evaluate side-chains 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049407 restraints weight = 12842.067| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.45 r_work: 0.2790 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.121 Angle : 0.448 5.943 5243 Z= 0.242 Chirality : 0.040 0.134 638 Planarity : 0.002 0.018 687 Dihedral : 3.670 17.998 552 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.50 % Allowed : 9.16 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.36), residues: 522 helix: 2.66 (0.29), residues: 299 sheet: 0.80 (0.58), residues: 80 loop : -0.16 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 362 TYR 0.007 0.001 TYR B 476 PHE 0.005 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3883) covalent geometry : angle 0.44780 ( 5243) hydrogen bonds : bond 0.04093 ( 267) hydrogen bonds : angle 4.09782 ( 765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.159 Fit side-chains REVERT: B 193 MET cc_start: 0.9183 (ttm) cc_final: 0.8965 (ttm) REVERT: B 307 MET cc_start: 0.8732 (mpp) cc_final: 0.8403 (mpp) REVERT: B 338 GLU cc_start: 0.8531 (tp30) cc_final: 0.8304 (tp30) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0501 time to fit residues: 1.6011 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.061543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047828 restraints weight = 12923.839| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.42 r_work: 0.2744 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3883 Z= 0.208 Angle : 0.494 6.139 5243 Z= 0.265 Chirality : 0.041 0.137 638 Planarity : 0.002 0.017 687 Dihedral : 3.743 17.795 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 10.40 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.36), residues: 522 helix: 2.63 (0.29), residues: 299 sheet: 0.94 (0.59), residues: 74 loop : -0.12 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.010 0.001 TYR B 506 PHE 0.007 0.001 PHE B 219 HIS 0.001 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 3883) covalent geometry : angle 0.49388 ( 5243) hydrogen bonds : bond 0.04391 ( 267) hydrogen bonds : angle 4.13327 ( 765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9196 (ttm) cc_final: 0.8987 (ttm) REVERT: B 307 MET cc_start: 0.8718 (mpp) cc_final: 0.8401 (mpp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0618 time to fit residues: 2.1073 Evaluate side-chains 24 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 330 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.061296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.047589 restraints weight = 12863.890| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.40 r_work: 0.2735 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3883 Z= 0.198 Angle : 0.499 6.859 5243 Z= 0.267 Chirality : 0.040 0.136 638 Planarity : 0.002 0.016 687 Dihedral : 3.778 17.745 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 11.14 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.36), residues: 522 helix: 2.62 (0.29), residues: 299 sheet: 0.98 (0.59), residues: 74 loop : -0.17 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.009 0.001 TYR B 506 PHE 0.007 0.001 PHE B 219 HIS 0.001 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 3883) covalent geometry : angle 0.49914 ( 5243) hydrogen bonds : bond 0.04360 ( 267) hydrogen bonds : angle 4.15876 ( 765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9200 (ttm) cc_final: 0.9000 (ttm) REVERT: B 307 MET cc_start: 0.8709 (mpp) cc_final: 0.8388 (mpp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0494 time to fit residues: 1.8000 Evaluate side-chains 23 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.0370 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.062355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048651 restraints weight = 13149.099| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.52 r_work: 0.2764 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.116 Angle : 0.458 8.168 5243 Z= 0.242 Chirality : 0.039 0.130 638 Planarity : 0.002 0.016 687 Dihedral : 3.712 17.985 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.73 % Allowed : 11.14 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.37), residues: 522 helix: 2.70 (0.29), residues: 299 sheet: 1.00 (0.59), residues: 80 loop : -0.16 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.008 0.001 TYR B 476 PHE 0.005 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3883) covalent geometry : angle 0.45841 ( 5243) hydrogen bonds : bond 0.03917 ( 267) hydrogen bonds : angle 4.05318 ( 765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8713 (mpp) cc_final: 0.8384 (mpp) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0583 time to fit residues: 2.3325 Evaluate side-chains 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.061407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047694 restraints weight = 13169.080| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.50 r_work: 0.2738 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3883 Z= 0.179 Angle : 0.493 8.675 5243 Z= 0.260 Chirality : 0.040 0.134 638 Planarity : 0.002 0.017 687 Dihedral : 3.765 17.576 552 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.36), residues: 522 helix: 2.67 (0.29), residues: 299 sheet: 1.08 (0.61), residues: 74 loop : -0.12 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.010 0.001 TYR B 506 PHE 0.008 0.001 PHE B 195 HIS 0.001 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3883) covalent geometry : angle 0.49300 ( 5243) hydrogen bonds : bond 0.04203 ( 267) hydrogen bonds : angle 4.10164 ( 765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8723 (mpp) cc_final: 0.8375 (mpp) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.0478 time to fit residues: 1.8889 Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.061822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047782 restraints weight = 12930.957| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.47 r_work: 0.2744 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3883 Z= 0.157 Angle : 0.482 9.391 5243 Z= 0.253 Chirality : 0.040 0.132 638 Planarity : 0.002 0.016 687 Dihedral : 3.787 17.763 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.36), residues: 522 helix: 2.61 (0.29), residues: 300 sheet: 1.06 (0.62), residues: 74 loop : -0.11 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 368 TYR 0.008 0.001 TYR B 506 PHE 0.006 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3883) covalent geometry : angle 0.48185 ( 5243) hydrogen bonds : bond 0.04082 ( 267) hydrogen bonds : angle 4.07679 ( 765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8714 (mpp) cc_final: 0.8368 (mpp) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0478 time to fit residues: 1.8366 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.061377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.047235 restraints weight = 12848.570| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.41 r_work: 0.2717 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3883 Z= 0.253 Angle : 0.565 9.631 5243 Z= 0.295 Chirality : 0.042 0.141 638 Planarity : 0.003 0.023 687 Dihedral : 3.967 17.660 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.36), residues: 522 helix: 2.51 (0.29), residues: 300 sheet: 0.97 (0.62), residues: 74 loop : -0.20 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.010 0.001 TYR B 506 PHE 0.008 0.001 PHE B 219 HIS 0.001 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 3883) covalent geometry : angle 0.56481 ( 5243) hydrogen bonds : bond 0.04634 ( 267) hydrogen bonds : angle 4.25193 ( 765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 307 MET cc_start: 0.8674 (mpp) cc_final: 0.8276 (mpp) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.0548 time to fit residues: 2.1782 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.062608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048495 restraints weight = 12904.442| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.44 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3883 Z= 0.143 Angle : 0.483 9.316 5243 Z= 0.253 Chirality : 0.039 0.130 638 Planarity : 0.002 0.015 687 Dihedral : 3.845 18.243 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.24 % Allowed : 11.88 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.36), residues: 522 helix: 2.60 (0.29), residues: 300 sheet: 0.82 (0.60), residues: 80 loop : -0.24 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 368 TYR 0.009 0.001 TYR B 199 PHE 0.005 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3883) covalent geometry : angle 0.48290 ( 5243) hydrogen bonds : bond 0.04066 ( 267) hydrogen bonds : angle 4.11945 ( 765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.161 Fit side-chains REVERT: B 307 MET cc_start: 0.8658 (mpp) cc_final: 0.8257 (mpp) REVERT: B 338 GLU cc_start: 0.8487 (tp30) cc_final: 0.8271 (tp30) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.0486 time to fit residues: 1.8543 Evaluate side-chains 26 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.062584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048583 restraints weight = 12767.759| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.42 r_work: 0.2765 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3883 Z= 0.137 Angle : 0.478 9.100 5243 Z= 0.249 Chirality : 0.039 0.130 638 Planarity : 0.002 0.015 687 Dihedral : 3.792 17.931 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.49 % Allowed : 11.63 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.37), residues: 522 helix: 2.60 (0.29), residues: 300 sheet: 0.83 (0.61), residues: 80 loop : -0.21 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 368 TYR 0.009 0.001 TYR B 199 PHE 0.006 0.001 PHE B 195 HIS 0.000 0.000 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3883) covalent geometry : angle 0.47768 ( 5243) hydrogen bonds : bond 0.03993 ( 267) hydrogen bonds : angle 4.08137 ( 765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 959.00 seconds wall clock time: 17 minutes 13.02 seconds (1033.02 seconds total)