Starting phenix.real_space_refine on Tue Feb 11 03:16:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoo_33354/02_2025/7xoo_33354.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.26, per 1000 atoms: 0.85 Number of scatterers: 3855 At special positions: 0 Unit cell: (69.6, 73.95, 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: 1.05 Conformation dependent library (CDL) restraints added in 479.2 milliseconds 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: 19 helices and 7 sheets defined 59.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.116A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 109 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 170 removed outlier: 3.598A 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 244 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 338 through 355 removed outlier: 3.812A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.218A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 409 Processing helix chain 'B' and resid 416 through 427 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 removed outlier: 6.423A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.373A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 323 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.373A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (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 479 270 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.13 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: 1339 1.34 - 1.46: 414 1.46 - 1.57: 2093 1.57 - 1.69: 0 1.69 - 1.80: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CB THR B 522 " pdb=" CG2 THR B 522 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB MET B 16 " pdb=" CG MET B 16 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.87e-01 bond pdb=" CB MET B 520 " pdb=" CG MET B 520 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 bond pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.46e-01 bond pdb=" C GLY B 70 " pdb=" O GLY B 70 " ideal model delta sigma weight residual 1.234 1.243 -0.010 1.21e-02 6.83e+03 6.31e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 5108 1.17 - 2.34: 102 2.34 - 3.52: 29 3.52 - 4.69: 1 4.69 - 5.86: 3 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 113.18 119.04 -5.86 2.37e+00 1.78e-01 6.12e+00 angle pdb=" N SER B 228 " pdb=" CA SER B 228 " pdb=" C SER B 228 " ideal model delta sigma weight residual 113.18 110.26 2.92 1.33e+00 5.65e-01 4.83e+00 angle pdb=" N ALA B 449 " pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 112.75 115.46 -2.71 1.36e+00 5.41e-01 3.98e+00 angle pdb=" N GLN B 351 " pdb=" CA GLN B 351 " pdb=" CB GLN B 351 " ideal model delta sigma weight residual 110.12 112.90 -2.78 1.47e+00 4.63e-01 3.58e+00 angle pdb=" CB MET B 69 " pdb=" CG MET B 69 " pdb=" SD MET B 69 " ideal model delta sigma weight residual 112.70 107.32 5.38 3.00e+00 1.11e-01 3.21e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 2218 15.66 - 31.31: 151 31.31 - 46.97: 35 46.97 - 62.62: 3 62.62 - 78.28: 5 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA GLU B 338 " pdb=" C GLU B 338 " pdb=" N GLU B 339 " pdb=" CA GLU B 339 " ideal model delta harmonic sigma weight residual 180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CG ARG B 421 " pdb=" CD ARG B 421 " pdb=" NE ARG B 421 " pdb=" CZ ARG B 421 " ideal model delta sinusoidal sigma weight residual 180.00 -138.97 -41.03 2 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" CG LYS B 132 " pdb=" CD LYS B 132 " pdb=" CE LYS B 132 " pdb=" NZ LYS B 132 " ideal model delta sinusoidal sigma weight residual -60.00 -107.83 47.83 3 1.50e+01 4.44e-03 8.55e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 395 0.028 - 0.057: 154 0.057 - 0.085: 50 0.085 - 0.114: 34 0.114 - 0.142: 5 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU B 102 " pdb=" N GLU B 102 " pdb=" C GLU B 102 " pdb=" CB GLU B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-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 3.65e-01 chirality pdb=" CA PRO B 462 " pdb=" N PRO B 462 " pdb=" C PRO B 462 " pdb=" CB PRO B 462 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 98 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C ALA B 98 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA B 98 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 233 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C MET B 233 " -0.019 2.00e-02 2.50e+03 pdb=" O MET B 233 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 449 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.20e-01 pdb=" N PRO B 450 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 450 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 450 " -0.013 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1284 2.85 - 3.36: 4021 3.36 - 3.87: 6325 3.87 - 4.39: 6853 4.39 - 4.90: 12172 Nonbonded interactions: 30655 Sorted by model distance: nonbonded pdb=" OD1 ASN B 479 " pdb=" OG1 THR B 482 " model vdw 2.333 3.040 nonbonded pdb=" OG SER B 135 " pdb=" OG1 THR B 497 " model vdw 2.339 3.040 nonbonded pdb=" OE2 GLU B 339 " pdb=" NE2 GLN B 343 " model vdw 2.374 3.120 nonbonded pdb=" O PHE B 219 " pdb=" N LEU B 248 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASN B 229 " pdb=" N ILE B 230 " model vdw 2.431 3.120 ... (remaining 30650 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 0.041 3883 Z= 0.214 Angle : 0.461 5.862 5243 Z= 0.255 Chirality : 0.039 0.142 638 Planarity : 0.002 0.023 687 Dihedral : 11.952 78.277 1464 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.36), residues: 522 helix: 2.86 (0.29), residues: 297 sheet: 0.25 (0.54), residues: 88 loop : 0.10 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.007 0.001 PHE B 195 TYR 0.008 0.001 TYR B 199 ARG 0.003 0.000 ARG B 404 *********************** 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 27 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: B 288 MET cc_start: 0.8613 (mtt) cc_final: 0.8396 (mtt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.6623 time to fit residues: 46.3581 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056146 restraints weight = 9396.197| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.85 r_work: 0.2758 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3883 Z= 0.145 Angle : 0.451 6.190 5243 Z= 0.246 Chirality : 0.040 0.156 638 Planarity : 0.002 0.020 687 Dihedral : 3.520 14.747 552 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.99 % Allowed : 5.20 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.37), residues: 522 helix: 2.95 (0.29), residues: 304 sheet: 0.13 (0.55), residues: 88 loop : -0.14 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.014 0.001 PHE B 195 TYR 0.005 0.001 TYR B 360 ARG 0.003 0.000 ARG B 421 *********************** 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 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.417 Fit side-chains REVERT: B 69 MET cc_start: 0.7375 (mtp) cc_final: 0.7024 (mtm) REVERT: B 362 ARG cc_start: 0.9170 (ttp80) cc_final: 0.8962 (ttp-110) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 1.6005 time to fit residues: 36.6103 Evaluate side-chains 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 522 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.076579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.051705 restraints weight = 9413.574| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.82 r_work: 0.2645 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3883 Z= 0.402 Angle : 0.535 6.724 5243 Z= 0.287 Chirality : 0.042 0.146 638 Planarity : 0.003 0.024 687 Dihedral : 3.801 16.387 552 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.25 % Allowed : 7.67 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.36), residues: 522 helix: 2.72 (0.28), residues: 302 sheet: 0.18 (0.59), residues: 80 loop : -0.24 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.010 0.001 PHE B 195 TYR 0.008 0.002 TYR B 199 ARG 0.002 0.000 ARG B 404 *********************** 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 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: B 518 GLU cc_start: 0.6687 (pt0) cc_final: 0.6043 (pt0) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 1.6141 time to fit residues: 35.3438 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.078983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054576 restraints weight = 9317.424| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.82 r_work: 0.2722 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3883 Z= 0.161 Angle : 0.440 7.437 5243 Z= 0.236 Chirality : 0.039 0.141 638 Planarity : 0.002 0.021 687 Dihedral : 3.597 15.492 552 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.74 % Allowed : 7.92 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.36), residues: 522 helix: 2.89 (0.28), residues: 302 sheet: 0.18 (0.57), residues: 88 loop : -0.32 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.013 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.002 0.000 ARG B 421 *********************** 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 25 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 518 GLU cc_start: 0.6696 (pt0) cc_final: 0.6003 (pt0) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 1.6157 time to fit residues: 41.8851 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.078208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053487 restraints weight = 9763.433| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.88 r_work: 0.2698 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3883 Z= 0.205 Angle : 0.460 8.288 5243 Z= 0.244 Chirality : 0.039 0.139 638 Planarity : 0.002 0.022 687 Dihedral : 3.602 15.802 552 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.74 % Allowed : 9.65 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.36), residues: 522 helix: 2.92 (0.29), residues: 302 sheet: 0.24 (0.57), residues: 88 loop : -0.33 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.012 0.001 PHE B 195 TYR 0.007 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** 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 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.398 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 1.4252 time to fit residues: 31.2823 Evaluate side-chains 19 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.076413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051515 restraints weight = 9540.589| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.84 r_work: 0.2645 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3883 Z= 0.348 Angle : 0.516 8.624 5243 Z= 0.272 Chirality : 0.041 0.143 638 Planarity : 0.003 0.024 687 Dihedral : 3.775 16.702 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.36), residues: 522 helix: 2.78 (0.29), residues: 302 sheet: 0.25 (0.57), residues: 88 loop : -0.35 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.007 0.001 TYR B 199 ARG 0.002 0.000 ARG B 345 *********************** 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 22 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.554 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 1.2660 time to fit residues: 29.2587 Evaluate side-chains 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.077427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.052761 restraints weight = 9584.055| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.84 r_work: 0.2675 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3883 Z= 0.239 Angle : 0.478 9.808 5243 Z= 0.251 Chirality : 0.039 0.142 638 Planarity : 0.002 0.023 687 Dihedral : 3.699 15.755 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.37), residues: 522 helix: 2.82 (0.29), residues: 302 sheet: 0.25 (0.58), residues: 88 loop : -0.36 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** 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 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.473 Fit side-chains REVERT: B 193 MET cc_start: 0.9249 (ptp) cc_final: 0.9029 (ptt) outliers start: 3 outliers final: 2 residues processed: 21 average time/residue: 1.3441 time to fit residues: 29.5874 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.078139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.053862 restraints weight = 9589.651| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.84 r_work: 0.2703 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.185 Angle : 0.478 10.956 5243 Z= 0.249 Chirality : 0.039 0.140 638 Planarity : 0.002 0.023 687 Dihedral : 3.615 14.487 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.50 % Allowed : 11.88 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.37), residues: 522 helix: 2.89 (0.29), residues: 302 sheet: 0.30 (0.59), residues: 88 loop : -0.39 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 368 *********************** 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 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.457 Fit side-chains REVERT: B 193 MET cc_start: 0.9227 (ptp) cc_final: 0.9001 (ptt) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 1.2200 time to fit residues: 26.9685 Evaluate side-chains 21 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 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 = 0.3397 r_free = 0.3397 target = 0.076861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.052115 restraints weight = 9707.938| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.87 r_work: 0.2658 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3883 Z= 0.304 Angle : 0.522 12.808 5243 Z= 0.272 Chirality : 0.040 0.143 638 Planarity : 0.003 0.024 687 Dihedral : 3.695 14.506 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.37), residues: 522 helix: 2.78 (0.29), residues: 302 sheet: 0.25 (0.59), residues: 88 loop : -0.30 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 401 PHE 0.010 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** 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 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.442 Fit side-chains REVERT: B 193 MET cc_start: 0.9232 (ptp) cc_final: 0.9001 (ptt) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 1.2463 time to fit residues: 26.3067 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.077646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052990 restraints weight = 9612.844| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.86 r_work: 0.2682 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3883 Z= 0.233 Angle : 0.499 13.129 5243 Z= 0.260 Chirality : 0.039 0.140 638 Planarity : 0.002 0.024 687 Dihedral : 3.647 14.235 552 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.50 % Allowed : 11.88 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.37), residues: 522 helix: 2.79 (0.28), residues: 302 sheet: 0.24 (0.59), residues: 88 loop : -0.33 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 368 ********************** 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 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.438 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 1.3531 time to fit residues: 28.4026 Evaluate side-chains 20 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 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 = 0.3411 r_free = 0.3411 target = 0.077516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052900 restraints weight = 9457.965| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.83 r_work: 0.2684 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2064 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= 0.231 Angle : 0.498 13.206 5243 Z= 0.259 Chirality : 0.039 0.141 638 Planarity : 0.002 0.024 687 Dihedral : 3.628 13.955 552 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.50 % Allowed : 12.13 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.37), residues: 522 helix: 2.81 (0.28), residues: 302 sheet: 0.27 (0.59), residues: 88 loop : -0.32 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.97 seconds wall clock time: 41 minutes 2.83 seconds (2462.83 seconds total)