Starting phenix.real_space_refine on Wed Mar 5 17:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qru_18626/03_2025/8qru_18626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qru_18626/03_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_18626/03_2025/8qru_18626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qru_18626/03_2025/8qru_18626.map" model { file = "/net/cci-nas-00/data/ceres_data/8qru_18626/03_2025/8qru_18626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qru_18626/03_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-5624/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: 2.50, per 1000 atoms: 0.81 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: 0.82 Conformation dependent library (CDL) restraints added in 385.9 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: 0.31 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: 0.85 Time building geometry restraints manager: 0.97 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.030 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- 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 : 0.342 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: 0.8500 time to fit residues: 48.6680 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 : 0.341 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107134 restraints weight = 3753.090| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.95 r_work: 0.3083 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.313 Fit side-chains REVERT: B 224 GLN cc_start: 0.7750 (mm110) cc_final: 0.7215 (pt0) REVERT: B 444 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7394 (mt-10) REVERT: B 483 GLN cc_start: 0.8623 (tp40) cc_final: 0.8392 (tp40) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.9137 time to fit residues: 59.6501 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 : 0.347 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 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: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.149975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104891 restraints weight = 3756.074| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.90 r_work: 0.3053 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3148 Z= 0.247 Angle : 0.592 5.275 4288 Z= 0.293 Chirality : 0.039 0.125 538 Planarity : 0.005 0.055 530 Dihedral : 4.448 38.189 435 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.98 % Allowed : 11.93 % Favored : 84.10 % 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: 1.82 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.26 (0.67), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 PHE 0.013 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 68 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.313 Fit side-chains REVERT: B 224 GLN cc_start: 0.7800 (mm110) cc_final: 0.7227 (pt0) REVERT: B 444 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7273 (mt-10) REVERT: B 483 GLN cc_start: 0.8690 (tp40) cc_final: 0.8271 (tp-100) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.9039 time to fit residues: 58.2127 Evaluate side-chains 53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.152026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.107362 restraints weight = 3860.112| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.90 r_work: 0.3090 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1993 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= 0.167 Angle : 0.543 5.832 4288 Z= 0.268 Chirality : 0.037 0.123 538 Planarity : 0.005 0.052 530 Dihedral : 4.452 40.842 435 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.67 % Allowed : 14.07 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.42), residues: 409 helix: 2.00 (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 0.006 0.001 PHE B 237 TYR 0.009 0.001 TYR B 485 ARG 0.007 0.001 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 69 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.342 Fit side-chains REVERT: B 120 ASP cc_start: 0.7111 (m-30) cc_final: 0.6473 (m-30) REVERT: B 224 GLN cc_start: 0.7780 (mm110) cc_final: 0.7294 (pt0) REVERT: B 246 ARG cc_start: 0.8873 (tpt170) cc_final: 0.8520 (tpt90) REVERT: B 483 GLN cc_start: 0.8742 (tp40) cc_final: 0.8317 (tp-100) REVERT: B 487 ASP cc_start: 0.5589 (m-30) cc_final: 0.5313 (m-30) outliers start: 12 outliers final: 3 residues processed: 63 average time/residue: 0.8409 time to fit residues: 55.1001 Evaluate side-chains 55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.151128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105414 restraints weight = 3804.230| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.95 r_work: 0.3073 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2112 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= 0.230 Angle : 0.574 6.544 4288 Z= 0.285 Chirality : 0.038 0.129 538 Planarity : 0.005 0.049 530 Dihedral : 4.302 34.435 435 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.75 % Allowed : 18.04 % Favored : 79.20 % 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: 1.86 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.32 (0.67), 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 373 PHE 0.016 0.002 PHE B 348 TYR 0.011 0.002 TYR B 485 ARG 0.006 0.001 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 61 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.283 Fit side-chains REVERT: B 126 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6978 (ptt90) REVERT: B 224 GLN cc_start: 0.7812 (mm110) cc_final: 0.7293 (pt0) REVERT: B 246 ARG cc_start: 0.8875 (tpt170) cc_final: 0.8615 (tpt90) REVERT: B 483 GLN cc_start: 0.8713 (tp40) cc_final: 0.8223 (tp-100) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.0162 time to fit residues: 62.9827 Evaluate side-chains 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 overall best weight: 0.9264 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.150435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104781 restraints weight = 3878.955| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.97 r_work: 0.3057 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2136 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= 0.230 Angle : 0.569 7.127 4288 Z= 0.282 Chirality : 0.038 0.128 538 Planarity : 0.005 0.047 530 Dihedral : 4.396 37.875 435 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.06 % Allowed : 19.57 % Favored : 77.37 % 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: 1.85 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.40 (0.66), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 130 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 237 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: 10 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: B 126 ARG cc_start: 0.7420 (mtm110) cc_final: 0.6924 (ptt90) REVERT: B 224 GLN cc_start: 0.7825 (mm110) cc_final: 0.7255 (pt0) REVERT: B 483 GLN cc_start: 0.8705 (tp40) cc_final: 0.8159 (tp-100) REVERT: B 487 ASP cc_start: 0.5724 (m-30) cc_final: 0.5450 (m-30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.9406 time to fit residues: 59.4614 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 : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.151330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105836 restraints weight = 3794.963| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.95 r_work: 0.3079 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2259 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= 0.201 Angle : 0.564 8.076 4288 Z= 0.279 Chirality : 0.037 0.127 538 Planarity : 0.005 0.045 530 Dihedral : 4.261 33.146 435 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 1.96 (0.41), residues: 409 helix: 1.86 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.57 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 130 HIS 0.003 0.001 HIS B 373 PHE 0.012 0.001 PHE B 348 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 : 0.341 Fit side-chains REVERT: B 126 ARG cc_start: 0.7452 (mtm110) cc_final: 0.7206 (ptm-80) REVERT: B 224 GLN cc_start: 0.7820 (mm110) cc_final: 0.7275 (pt0) REVERT: B 376 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7773 (mtm-85) REVERT: B 444 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7172 (mt-10) REVERT: B 483 GLN cc_start: 0.8693 (tp40) cc_final: 0.8089 (tp-100) REVERT: B 487 ASP cc_start: 0.5851 (m-30) cc_final: 0.5640 (m-30) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.9550 time to fit residues: 61.2643 Evaluate side-chains 60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.149607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104057 restraints weight = 3825.010| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.94 r_work: 0.3041 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2268 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= 0.255 Angle : 0.595 9.053 4288 Z= 0.294 Chirality : 0.038 0.128 538 Planarity : 0.005 0.044 530 Dihedral : 4.410 39.918 435 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.14 % Allowed : 21.10 % Favored : 76.76 % 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: 1.80 (0.41), residues: 409 helix: 1.77 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.68 (0.63), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 130 HIS 0.001 0.000 HIS B 373 PHE 0.011 0.001 PHE B 237 TYR 0.012 0.002 TYR B 485 ARG 0.009 0.000 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 58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.345 Fit side-chains REVERT: B 126 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7076 (ptt90) REVERT: B 224 GLN cc_start: 0.7883 (mm110) cc_final: 0.7336 (pt0) REVERT: B 376 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7853 (mtm-85) REVERT: B 444 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7236 (mt-10) REVERT: B 483 GLN cc_start: 0.8810 (tp40) cc_final: 0.8117 (tp-100) outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 1.0289 time to fit residues: 61.6689 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 : 0.331 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.151243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106111 restraints weight = 3805.737| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.92 r_work: 0.3073 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2363 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= 0.206 Angle : 0.575 10.119 4288 Z= 0.281 Chirality : 0.037 0.125 538 Planarity : 0.005 0.043 530 Dihedral : 4.432 41.883 435 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.45 % Allowed : 20.80 % Favored : 76.76 % 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: 1.85 (0.41), residues: 409 helix: 1.82 (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 0.013 0.001 TRP B 130 HIS 0.001 0.000 HIS B 316 PHE 0.009 0.001 PHE B 237 TYR 0.007 0.002 TYR B 485 ARG 0.009 0.001 ARG B 335 *********************** 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 59 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.338 Fit side-chains REVERT: B 126 ARG cc_start: 0.7435 (mtm110) cc_final: 0.7105 (ptt90) REVERT: B 224 GLN cc_start: 0.7866 (mm110) cc_final: 0.7343 (pt0) REVERT: B 444 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7222 (mt-10) REVERT: B 483 GLN cc_start: 0.8782 (tp40) cc_final: 0.8185 (tp-100) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.9930 time to fit residues: 59.6090 Evaluate side-chains 54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.150366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104800 restraints weight = 3777.126| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.94 r_work: 0.3062 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2434 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= 0.227 Angle : 0.591 10.522 4288 Z= 0.288 Chirality : 0.038 0.125 538 Planarity : 0.005 0.043 530 Dihedral : 4.543 46.720 435 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.83 % Allowed : 22.32 % Favored : 75.84 % 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: 1.82 (0.41), residues: 409 helix: 1.80 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.73 (0.63), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 130 HIS 0.001 0.000 HIS B 316 PHE 0.016 0.001 PHE B 326 TYR 0.008 0.002 TYR B 204 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 59 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.343 Fit side-chains REVERT: B 126 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7069 (ptt90) REVERT: B 224 GLN cc_start: 0.7848 (mm110) cc_final: 0.7272 (pt0) REVERT: B 301 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7857 (tmt-80) REVERT: B 444 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7215 (mt-10) REVERT: B 483 GLN cc_start: 0.8667 (tp40) cc_final: 0.8182 (tp-100) REVERT: B 601 GLN cc_start: 0.7737 (mm110) cc_final: 0.7521 (mm-40) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 1.0734 time to fit residues: 64.2593 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 104 ILE 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: 0.3980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108157 restraints weight = 3792.636| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.94 r_work: 0.3108 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2568 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 : 0.571 10.622 4288 Z= 0.278 Chirality : 0.037 0.158 538 Planarity : 0.005 0.042 530 Dihedral : 4.499 46.609 435 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.83 % Allowed : 22.94 % 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: 1.99 (0.41), residues: 409 helix: 1.93 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.80 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 130 HIS 0.003 0.001 HIS B 373 PHE 0.007 0.001 PHE B 237 TYR 0.007 0.001 TYR B 208 ARG 0.013 0.001 ARG B 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.04 seconds wall clock time: 47 minutes 31.62 seconds (2851.62 seconds total)