Starting phenix.real_space_refine on Mon Feb 10 22:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.map" model { file = "/net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qru_18626/02_2025/8qru_18626.cif" } resolution = 2.9 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= 1.000 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 15 5.16 5 C 2034 2.51 5 N 504 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 3093 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 16, 'TRANS': 398} Chain breaks: 2 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.47, per 1000 atoms: 0.80 Number of scatterers: 3093 At special positions: 0 Unit cell: (61.028, 67.716, 71.896, 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 15 16.00 O 540 8.00 N 504 7.00 C 2034 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: 0.73 Conformation dependent library (CDL) restraints added in 351.5 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 86.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 49 through 75 Processing helix chain 'B' and resid 76 through 117 removed outlier: 3.549A pdb=" N ALA B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Proline residue: B 83 - end of helix removed outlier: 3.756A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 4.364A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 126 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.711A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 292 removed outlier: 3.704A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.844A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.713A pdb=" N ALA B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.518A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 4.124A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 410 through 427 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.743A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 487 removed outlier: 3.670A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209 250 hydrogen bonds defined for protein. 747 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: 0.82 Time building geometry restraints manager: 0.86 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: 978 1.34 - 1.46: 660 1.46 - 1.58: 1486 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3148 Sorted by residual: bond pdb=" N GLN B 601 " pdb=" CA GLN B 601 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" CG PRO B 83 " pdb=" CD PRO B 83 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.47e+00 bond pdb=" CB PRO B 83 " pdb=" CG PRO B 83 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.42e+00 bond pdb=" C LEU B 379 " pdb=" O LEU B 379 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 5.13e-01 bond pdb=" CB PHE B 348 " pdb=" CG PHE B 348 " ideal model delta sigma weight residual 1.502 1.518 -0.016 2.30e-02 1.89e+03 4.93e-01 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 3996 0.85 - 1.70: 219 1.70 - 2.55: 44 2.55 - 3.40: 17 3.40 - 4.25: 12 Bond angle restraints: 4288 Sorted by residual: angle pdb=" N VAL B 446 " pdb=" CA VAL B 446 " pdb=" C VAL B 446 " ideal model delta sigma weight residual 112.17 109.18 2.99 9.50e-01 1.11e+00 9.88e+00 angle pdb=" CA PRO B 83 " pdb=" N PRO B 83 " pdb=" CD PRO B 83 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.23e+00 angle pdb=" N GLN B 403 " pdb=" CA GLN B 403 " pdb=" C GLN B 403 " ideal model delta sigma weight residual 114.04 111.58 2.46 1.24e+00 6.50e-01 3.93e+00 angle pdb=" CA GLU B 210 " pdb=" C GLU B 210 " pdb=" N ARG B 211 " ideal model delta sigma weight residual 114.76 116.86 -2.10 1.14e+00 7.69e-01 3.41e+00 angle pdb=" CA GLU B 210 " pdb=" C GLU B 210 " pdb=" O GLU B 210 " ideal model delta sigma weight residual 122.64 120.55 2.09 1.25e+00 6.40e-01 2.80e+00 ... (remaining 4283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1657 16.41 - 32.82: 150 32.82 - 49.23: 25 49.23 - 65.64: 11 65.64 - 82.05: 2 Dihedral angle restraints: 1845 sinusoidal: 674 harmonic: 1171 Sorted by residual: dihedral pdb=" CA PHE B 400 " pdb=" C PHE B 400 " pdb=" N ILE B 401 " pdb=" CA ILE B 401 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CG ARG B 376 " pdb=" CD ARG B 376 " pdb=" NE ARG B 376 " pdb=" CZ ARG B 376 " ideal model delta sinusoidal sigma weight residual -180.00 -136.07 -43.93 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ILE B 401 " pdb=" C ILE B 401 " pdb=" N ALA B 402 " pdb=" CA ALA B 402 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 354 0.026 - 0.052: 93 0.052 - 0.078: 62 0.078 - 0.104: 25 0.104 - 0.130: 4 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA PRO B 432 " pdb=" N PRO B 432 " pdb=" C PRO B 432 " pdb=" CB PRO B 432 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA ILE B 401 " pdb=" N ILE B 401 " pdb=" C ILE B 401 " pdb=" CB ILE B 401 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.80e-01 ... (remaining 535 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 82 " 0.061 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO B 83 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 342 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO B 343 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 343 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 343 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 431 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 432 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.017 5.00e-02 4.00e+02 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 708 2.79 - 3.31: 3336 3.31 - 3.84: 5327 3.84 - 4.37: 6035 4.37 - 4.90: 10768 Nonbonded interactions: 26174 Sorted by model distance: nonbonded pdb=" O ARG B 126 " pdb=" CD1 TRP B 130 " model vdw 2.257 3.260 nonbonded pdb=" OD1 ASP B 120 " pdb=" NH2 ARG B 246 " model vdw 2.283 3.120 nonbonded pdb=" NE1 TRP B 130 " pdb=" OH TYR B 485 " model vdw 2.314 3.120 nonbonded pdb=" O THR B 416 " pdb=" OG1 THR B 420 " model vdw 2.347 3.040 nonbonded pdb=" O GLN B 483 " pdb=" NE2 GLN B 483 " model vdw 2.431 3.120 ... (remaining 26169 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: 0.570 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.060 3148 Z= 0.165 Angle : 0.521 4.252 4288 Z= 0.298 Chirality : 0.036 0.130 538 Planarity : 0.006 0.091 530 Dihedral : 13.619 82.049 1093 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.61 % Allowed : 11.62 % Favored : 87.77 % 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: 1.76 (0.43), residues: 409 helix: 1.69 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.17 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.002 0.001 HIS B 313 PHE 0.007 0.001 PHE B 237 TYR 0.007 0.001 TYR B 485 ARG 0.003 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.306 Fit side-chains REVERT: B 182 ASP cc_start: 0.8289 (m-30) cc_final: 0.8086 (m-30) REVERT: B 224 GLN cc_start: 0.7623 (mm110) cc_final: 0.7315 (pt0) REVERT: B 229 MET cc_start: 0.9156 (ttm) cc_final: 0.8943 (ttm) REVERT: B 483 GLN cc_start: 0.8782 (tp40) cc_final: 0.8385 (tp-100) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.8821 time to fit residues: 50.4827 Evaluate side-chains 50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107147 restraints weight = 3753.090| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.95 r_work: 0.3084 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.192 Angle : 0.566 5.721 4288 Z= 0.281 Chirality : 0.038 0.125 538 Planarity : 0.006 0.058 530 Dihedral : 4.206 26.771 435 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.06 % Allowed : 11.31 % Favored : 85.63 % 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: 1.92 (0.41), residues: 409 helix: 1.81 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.29 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 130 HIS 0.002 0.001 HIS B 373 PHE 0.009 0.001 PHE B 237 TYR 0.005 0.001 TYR B 276 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.327 Fit side-chains REVERT: B 224 GLN cc_start: 0.7745 (mm110) cc_final: 0.7212 (pt0) REVERT: B 444 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7395 (mt-10) REVERT: B 483 GLN cc_start: 0.8622 (tp40) cc_final: 0.8392 (tp40) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.9261 time to fit residues: 60.4494 Evaluate side-chains 52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104453 restraints weight = 3756.404| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.91 r_work: 0.3050 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3148 Z= 0.260 Angle : 0.599 5.427 4288 Z= 0.296 Chirality : 0.039 0.127 538 Planarity : 0.005 0.055 530 Dihedral : 4.435 37.171 435 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.98 % Allowed : 11.62 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.41), residues: 409 helix: 1.80 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.26 (0.68), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 461 HIS 0.002 0.001 HIS B 373 PHE 0.014 0.002 PHE B 326 TYR 0.007 0.002 TYR B 276 ARG 0.007 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.342 Fit side-chains REVERT: B 224 GLN cc_start: 0.7803 (mm110) cc_final: 0.7254 (pt0) REVERT: B 444 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7273 (mt-10) REVERT: B 483 GLN cc_start: 0.8682 (tp40) cc_final: 0.8394 (tp40) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.8662 time to fit residues: 53.2094 Evaluate side-chains 52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106979 restraints weight = 3861.548| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.91 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3148 Z= 0.170 Angle : 0.549 5.799 4288 Z= 0.269 Chirality : 0.037 0.122 538 Planarity : 0.005 0.051 530 Dihedral : 4.436 41.226 435 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.06 % Allowed : 14.98 % Favored : 81.96 % 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: 2.14 (0.42), residues: 409 helix: 1.97 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.30 (0.65), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 130 HIS 0.001 0.000 HIS B 452 PHE 0.020 0.001 PHE B 348 TYR 0.008 0.001 TYR B 485 ARG 0.007 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.324 Fit side-chains REVERT: B 120 ASP cc_start: 0.7113 (m-30) cc_final: 0.6547 (m-30) REVERT: B 224 GLN cc_start: 0.7794 (mm110) cc_final: 0.7316 (pt0) REVERT: B 246 ARG cc_start: 0.8874 (tpt170) cc_final: 0.8524 (tpt90) REVERT: B 444 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7136 (mt-10) REVERT: B 483 GLN cc_start: 0.8714 (tp40) cc_final: 0.8205 (tp-100) REVERT: B 487 ASP cc_start: 0.5602 (m-30) cc_final: 0.5316 (m-30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.8850 time to fit residues: 56.1008 Evaluate side-chains 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105741 restraints weight = 3793.141| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.93 r_work: 0.3069 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3148 Z= 0.228 Angle : 0.567 6.416 4288 Z= 0.282 Chirality : 0.038 0.129 538 Planarity : 0.005 0.049 530 Dihedral : 4.287 33.819 435 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.75 % Allowed : 16.82 % Favored : 80.43 % 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: 2.01 (0.41), residues: 409 helix: 1.87 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.35 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 130 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE B 237 TYR 0.011 0.002 TYR B 485 ARG 0.006 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.323 Fit side-chains REVERT: B 126 ARG cc_start: 0.7400 (mtm110) cc_final: 0.6977 (ptt90) REVERT: B 224 GLN cc_start: 0.7801 (mm110) cc_final: 0.7273 (pt0) REVERT: B 246 ARG cc_start: 0.8870 (tpt170) cc_final: 0.8597 (tpt90) REVERT: B 483 GLN cc_start: 0.8707 (tp40) cc_final: 0.8206 (tp-100) REVERT: B 487 ASP cc_start: 0.5613 (m-30) cc_final: 0.5383 (m-30) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 1.0495 time to fit residues: 65.0940 Evaluate side-chains 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 413 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107289 restraints weight = 3887.092| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.97 r_work: 0.3095 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3148 Z= 0.168 Angle : 0.543 7.260 4288 Z= 0.268 Chirality : 0.037 0.124 538 Planarity : 0.005 0.046 530 Dihedral : 4.299 36.386 435 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.75 % Allowed : 18.96 % Favored : 78.29 % 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: 2.15 (0.41), residues: 409 helix: 1.99 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.48 (0.64), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 130 HIS 0.002 0.000 HIS B 373 PHE 0.020 0.001 PHE B 348 TYR 0.009 0.002 TYR B 485 ARG 0.008 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.350 Fit side-chains REVERT: B 126 ARG cc_start: 0.7437 (mtm110) cc_final: 0.6943 (ptt90) REVERT: B 224 GLN cc_start: 0.7766 (mm110) cc_final: 0.7277 (pt0) REVERT: B 483 GLN cc_start: 0.8719 (tp40) cc_final: 0.8178 (tp-100) REVERT: B 487 ASP cc_start: 0.5854 (m-30) cc_final: 0.5651 (m-30) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.8713 time to fit residues: 54.2397 Evaluate side-chains 55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106033 restraints weight = 3805.100| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.93 r_work: 0.3068 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3148 Z= 0.218 Angle : 0.571 8.157 4288 Z= 0.281 Chirality : 0.038 0.128 538 Planarity : 0.005 0.044 530 Dihedral : 4.234 32.823 435 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.45 % Allowed : 20.49 % Favored : 77.06 % 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: 2.00 (0.41), residues: 409 helix: 1.90 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS B 373 PHE 0.011 0.001 PHE B 237 TYR 0.011 0.002 TYR B 485 ARG 0.009 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.320 Fit side-chains REVERT: B 126 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7208 (ptm-80) REVERT: B 224 GLN cc_start: 0.7840 (mm110) cc_final: 0.7358 (pt0) REVERT: B 483 GLN cc_start: 0.8751 (tp40) cc_final: 0.8132 (tp-100) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.9262 time to fit residues: 59.5398 Evaluate side-chains 57 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 413 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106672 restraints weight = 3820.322| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.96 r_work: 0.3086 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3148 Z= 0.199 Angle : 0.566 9.034 4288 Z= 0.275 Chirality : 0.038 0.130 538 Planarity : 0.005 0.043 530 Dihedral : 4.333 37.356 435 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.75 % Allowed : 20.18 % Favored : 77.06 % 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: 1.97 (0.41), residues: 409 helix: 1.88 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.65 (0.63), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 PHE 0.021 0.001 PHE B 348 TYR 0.013 0.002 TYR B 485 ARG 0.009 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.343 Fit side-chains REVERT: B 126 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7095 (ptt90) REVERT: B 224 GLN cc_start: 0.7790 (mm110) cc_final: 0.7263 (pt0) REVERT: B 444 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7124 (mt-10) REVERT: B 483 GLN cc_start: 0.8712 (tp40) cc_final: 0.8099 (tp-100) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.8920 time to fit residues: 56.4073 Evaluate side-chains 58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107157 restraints weight = 3809.577| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.95 r_work: 0.3097 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.003 0.028 3148 Z= 0.189 Angle : 0.577 9.845 4288 Z= 0.282 Chirality : 0.037 0.142 538 Planarity : 0.006 0.052 530 Dihedral : 4.368 39.378 435 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.53 % Allowed : 22.02 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.41), residues: 409 helix: 1.92 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.75 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 130 HIS 0.001 0.000 HIS B 316 PHE 0.013 0.001 PHE B 326 TYR 0.010 0.002 TYR B 485 ARG 0.012 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.315 Fit side-chains REVERT: B 126 ARG cc_start: 0.7419 (mtm110) cc_final: 0.7091 (ptt90) REVERT: B 224 GLN cc_start: 0.7792 (mm110) cc_final: 0.7283 (pt0) REVERT: B 444 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7159 (mt-10) REVERT: B 483 GLN cc_start: 0.8705 (tp40) cc_final: 0.8283 (tp-100) outliers start: 5 outliers final: 6 residues processed: 56 average time/residue: 1.0117 time to fit residues: 58.5692 Evaluate side-chains 53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106959 restraints weight = 3775.635| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.92 r_work: 0.3091 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.211 Angle : 0.599 10.264 4288 Z= 0.293 Chirality : 0.038 0.161 538 Planarity : 0.005 0.042 530 Dihedral : 4.387 40.085 435 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.14 % Allowed : 22.63 % Favored : 75.23 % 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: 1.93 (0.41), residues: 409 helix: 1.88 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.76 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 130 HIS 0.002 0.001 HIS B 373 PHE 0.022 0.001 PHE B 348 TYR 0.009 0.002 TYR B 485 ARG 0.009 0.001 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.298 Fit side-chains REVERT: B 126 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7072 (ptt90) REVERT: B 224 GLN cc_start: 0.7834 (mm110) cc_final: 0.7360 (pt0) REVERT: B 301 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7936 (tmt-80) REVERT: B 483 GLN cc_start: 0.8661 (tp40) cc_final: 0.8351 (tp-100) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.9178 time to fit residues: 57.1155 Evaluate side-chains 55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108694 restraints weight = 3794.662| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.93 r_work: 0.3117 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3148 Z= 0.198 Angle : 0.619 10.643 4288 Z= 0.299 Chirality : 0.038 0.137 538 Planarity : 0.005 0.041 530 Dihedral : 4.363 41.156 435 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.53 % Allowed : 23.24 % Favored : 75.23 % 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: 1.94 (0.41), residues: 409 helix: 1.90 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.78 (0.61), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 PHE 0.013 0.001 PHE B 326 TYR 0.006 0.002 TYR B 208 ARG 0.009 0.001 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.80 seconds wall clock time: 45 minutes 5.07 seconds (2705.07 seconds total)