Starting phenix.real_space_refine on Wed Mar 5 23:49:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.map" model { file = "/net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz7_40902/03_2025/8sz7_40902.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 1285 2.51 5 N 341 2.21 5 O 365 1.98 5 H 2021 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4026 Number of models: 1 Model: "" Number of chains: 1 Chain: "g" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 4026 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 3 Time building chain proxies: 5.95, per 1000 atoms: 1.48 Number of scatterers: 4026 At special positions: 0 Unit cell: (88.941, 83.785, 77.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 365 8.00 N 341 7.00 C 1285 6.00 H 2021 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 265.1 milliseconds 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 50.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'g' and resid 369 through 374 Processing helix chain 'g' and resid 380 through 397 removed outlier: 3.639A pdb=" N GLY g 397 " --> pdb=" O LYS g 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 406 through 418 Processing helix chain 'g' and resid 420 through 430 removed outlier: 3.522A pdb=" N CYS g 424 " --> pdb=" O ILE g 420 " (cutoff:3.500A) Processing helix chain 'g' and resid 470 through 481 Processing helix chain 'g' and resid 482 through 484 No H-bonds generated for 'chain 'g' and resid 482 through 484' Processing helix chain 'g' and resid 532 through 536 Processing helix chain 'g' and resid 599 through 602 removed outlier: 3.506A pdb=" N GLN g 602 " --> pdb=" O ASP g 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 599 through 602' Processing helix chain 'g' and resid 609 through 624 removed outlier: 3.551A pdb=" N VAL g 613 " --> pdb=" O THR g 609 " (cutoff:3.500A) Processing helix chain 'g' and resid 654 through 687 removed outlier: 3.506A pdb=" N GLN g 658 " --> pdb=" O GLN g 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE g 672 " --> pdb=" O SER g 668 " (cutoff:3.500A) Proline residue: g 682 - end of helix removed outlier: 3.837A pdb=" N MET g 686 " --> pdb=" O PRO g 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'g' and resid 563 through 566 removed outlier: 3.786A pdb=" N TYR g 563 " --> pdb=" O TRP g 552 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR g 527 " --> pdb=" O ALA g 606 " (cutoff:3.500A) 97 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2018 1.03 - 1.23: 3 1.23 - 1.42: 846 1.42 - 1.61: 1171 1.61 - 1.81: 25 Bond restraints: 4063 Sorted by residual: bond pdb=" CA ASN g 363 " pdb=" C ASN g 363 " ideal model delta sigma weight residual 1.522 1.481 0.040 1.72e-02 3.38e+03 5.50e+00 bond pdb=" C ASN g 363 " pdb=" O ASN g 363 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.47e-02 4.63e+03 3.70e-01 bond pdb=" C VAL g 375 " pdb=" O VAL g 375 " ideal model delta sigma weight residual 1.236 1.227 0.008 1.47e-02 4.63e+03 3.12e-01 bond pdb=" CB LYS g 683 " pdb=" CG LYS g 683 " ideal model delta sigma weight residual 1.520 1.503 0.017 3.00e-02 1.11e+03 3.04e-01 bond pdb=" CB ARG g 364 " pdb=" CG ARG g 364 " ideal model delta sigma weight residual 1.520 1.504 0.016 3.00e-02 1.11e+03 2.72e-01 ... (remaining 4058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 7341 6.26 - 12.51: 1 12.51 - 18.77: 0 18.77 - 25.03: 0 25.03 - 31.29: 5 Bond angle restraints: 7347 Sorted by residual: angle pdb=" CG TRP g 552 " pdb=" CB TRP g 552 " pdb=" HB3 TRP g 552 " ideal model delta sigma weight residual 108.00 76.71 31.29 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CG TRP g 552 " pdb=" CB TRP g 552 " pdb=" HB2 TRP g 552 " ideal model delta sigma weight residual 108.00 78.96 29.04 3.00e+00 1.11e-01 9.37e+01 angle pdb=" CA TRP g 552 " pdb=" CB TRP g 552 " pdb=" HB3 TRP g 552 " ideal model delta sigma weight residual 109.00 81.27 27.73 3.00e+00 1.11e-01 8.55e+01 angle pdb=" HB2 TRP g 552 " pdb=" CB TRP g 552 " pdb=" HB3 TRP g 552 " ideal model delta sigma weight residual 110.00 137.42 -27.42 3.00e+00 1.11e-01 8.35e+01 angle pdb=" CA TRP g 552 " pdb=" CB TRP g 552 " pdb=" HB2 TRP g 552 " ideal model delta sigma weight residual 109.00 82.31 26.69 3.00e+00 1.11e-01 7.92e+01 ... (remaining 7342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1819 17.98 - 35.97: 42 35.97 - 53.95: 13 53.95 - 71.93: 4 71.93 - 89.92: 2 Dihedral angle restraints: 1880 sinusoidal: 1035 harmonic: 845 Sorted by residual: dihedral pdb=" CA ILE g 365 " pdb=" C ILE g 365 " pdb=" N PHE g 366 " pdb=" CA PHE g 366 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA HIS g 367 " pdb=" C HIS g 367 " pdb=" N GLU g 368 " pdb=" CA GLU g 368 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ARG g 364 " pdb=" C ARG g 364 " pdb=" N ILE g 365 " pdb=" CA ILE g 365 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 1877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 158 0.024 - 0.049: 92 0.049 - 0.073: 31 0.073 - 0.097: 8 0.097 - 0.122: 7 Chirality restraints: 296 Sorted by residual: chirality pdb=" CA ILE g 528 " pdb=" N ILE g 528 " pdb=" C ILE g 528 " pdb=" CB ILE g 528 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA VAL g 544 " pdb=" N VAL g 544 " pdb=" C VAL g 544 " pdb=" CB VAL g 544 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ASN g 363 " pdb=" N ASN g 363 " pdb=" C ASN g 363 " pdb=" CB ASN g 363 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.85e-01 ... (remaining 293 not shown) Planarity restraints: 575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE g 370 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.52e-01 pdb=" N PRO g 371 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO g 371 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO g 371 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS g 367 " -0.003 2.00e-02 2.50e+03 6.90e-03 4.76e-01 pdb=" C HIS g 367 " 0.012 2.00e-02 2.50e+03 pdb=" O HIS g 367 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU g 368 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR g 626 " -0.010 5.00e-02 4.00e+02 1.57e-02 3.93e-01 pdb=" N PRO g 627 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO g 627 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO g 627 " -0.009 5.00e-02 4.00e+02 ... (remaining 572 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 161 2.19 - 2.79: 8256 2.79 - 3.40: 10479 3.40 - 4.00: 13142 4.00 - 4.60: 20563 Nonbonded interactions: 52601 Sorted by model distance: nonbonded pdb=" OE1 GLN g 654 " pdb=" H GLN g 654 " model vdw 1.592 2.450 nonbonded pdb=" H ILE g 521 " pdb=" O LEU g 545 " model vdw 1.693 2.450 nonbonded pdb=" HA TRP g 552 " pdb=" HB3 TRP g 552 " model vdw 1.717 1.952 nonbonded pdb=" HZ3 LYS g 554 " pdb=" OD2 ASP g 555 " model vdw 1.760 2.450 nonbonded pdb=" O LEU g 680 " pdb=" H THR g 684 " model vdw 1.783 2.450 ... (remaining 52596 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: 44.310 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.600 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:14.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2048 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 0.040 2042 Z= 0.166 Angle : 0.458 7.750 2736 Z= 0.266 Chirality : 0.036 0.122 296 Planarity : 0.002 0.023 344 Dihedral : 9.672 89.915 788 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 1.11 (0.55), residues: 232 helix: 1.53 (0.53), residues: 105 sheet: 0.87 (0.81), residues: 38 loop : -0.22 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP g 542 HIS 0.004 0.001 HIS g 490 PHE 0.006 0.001 PHE g 409 TYR 0.009 0.001 TYR g 485 ARG 0.001 0.000 ARG g 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 2.5109 time to fit residues: 118.3506 Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.293276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.252122 restraints weight = 7844.036| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.65 r_work: 0.4325 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2042 Z= 0.291 Angle : 0.664 7.594 2736 Z= 0.369 Chirality : 0.041 0.158 296 Planarity : 0.005 0.044 344 Dihedral : 4.431 21.189 260 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.45 % Allowed : 8.14 % Favored : 91.40 % 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: 1.62 (0.55), residues: 232 helix: 2.35 (0.52), residues: 107 sheet: 1.03 (0.82), residues: 38 loop : -0.55 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP g 616 HIS 0.005 0.001 HIS g 367 PHE 0.016 0.002 PHE g 366 TYR 0.014 0.002 TYR g 597 ARG 0.004 0.001 ARG g 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8014 (mt) cc_final: 0.7801 (mm) REVERT: g 549 ASN cc_start: 0.7407 (p0) cc_final: 0.7089 (p0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 1.3883 time to fit residues: 61.8607 Evaluate side-chains 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 2 optimal weight: 0.0570 chunk 6 optimal weight: 0.0370 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 658 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.294753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.252532 restraints weight = 7768.335| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.61 r_work: 0.4234 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4123 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2042 Z= 0.192 Angle : 0.559 7.562 2736 Z= 0.307 Chirality : 0.037 0.132 296 Planarity : 0.004 0.036 344 Dihedral : 4.196 16.882 260 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.45 % Allowed : 11.31 % Favored : 88.24 % 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: 1.83 (0.56), residues: 232 helix: 2.26 (0.52), residues: 112 sheet: 1.08 (0.81), residues: 38 loop : -0.17 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP g 542 HIS 0.004 0.001 HIS g 367 PHE 0.015 0.001 PHE g 620 TYR 0.010 0.001 TYR g 485 ARG 0.002 0.000 ARG g 573 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8067 (mt) cc_final: 0.7829 (mm) REVERT: g 549 ASN cc_start: 0.7418 (p0) cc_final: 0.7047 (p0) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 2.7093 time to fit residues: 112.0229 Evaluate side-chains 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.0040 overall best weight: 0.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.293705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.250919 restraints weight = 7751.916| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.19 r_work: 0.4233 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2042 Z= 0.219 Angle : 0.572 7.695 2736 Z= 0.314 Chirality : 0.037 0.138 296 Planarity : 0.004 0.040 344 Dihedral : 4.202 19.298 260 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.36 % Allowed : 11.76 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.55), residues: 232 helix: 2.21 (0.51), residues: 112 sheet: 0.98 (0.79), residues: 38 loop : -0.15 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 542 HIS 0.004 0.001 HIS g 367 PHE 0.015 0.001 PHE g 620 TYR 0.010 0.001 TYR g 485 ARG 0.001 0.000 ARG g 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8196 (mt) cc_final: 0.7963 (mm) REVERT: g 549 ASN cc_start: 0.7538 (p0) cc_final: 0.7186 (p0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 2.5856 time to fit residues: 104.7022 Evaluate side-chains 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.0870 chunk 2 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.293432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.238725 restraints weight = 8072.629| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 4.49 r_work: 0.4203 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4104 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2042 Z= 0.236 Angle : 0.594 7.912 2736 Z= 0.324 Chirality : 0.038 0.135 296 Planarity : 0.005 0.044 344 Dihedral : 4.253 21.566 260 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.81 % Allowed : 10.86 % Favored : 87.33 % 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: 1.39 (0.55), residues: 232 helix: 2.05 (0.52), residues: 110 sheet: 0.88 (0.78), residues: 38 loop : -0.58 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP g 542 HIS 0.004 0.001 HIS g 367 PHE 0.010 0.001 PHE g 620 TYR 0.011 0.001 TYR g 485 ARG 0.001 0.000 ARG g 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8266 (mt) cc_final: 0.7994 (mm) REVERT: g 549 ASN cc_start: 0.7696 (p0) cc_final: 0.7306 (p0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 1.6334 time to fit residues: 64.0664 Evaluate side-chains 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 365 ILE Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.0980 overall best weight: 0.0972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.294402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.238387 restraints weight = 7862.214| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 4.49 r_work: 0.4208 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4100 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2042 Z= 0.157 Angle : 0.530 8.091 2736 Z= 0.288 Chirality : 0.036 0.135 296 Planarity : 0.004 0.040 344 Dihedral : 4.163 19.962 260 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 11.76 % Favored : 87.33 % 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: 1.73 (0.55), residues: 232 helix: 2.38 (0.52), residues: 112 sheet: 0.78 (0.77), residues: 38 loop : -0.41 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 PHE 0.008 0.001 PHE g 620 TYR 0.008 0.001 TYR g 485 ARG 0.001 0.000 ARG g 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8205 (mt) cc_final: 0.7948 (mm) REVERT: g 549 ASN cc_start: 0.7673 (p0) cc_final: 0.7292 (p0) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 1.7001 time to fit residues: 59.5241 Evaluate side-chains 34 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Chi-restraints excluded: chain g residue 580 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 0.0770 chunk 5 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 0.0980 chunk 21 optimal weight: 0.0070 chunk 22 optimal weight: 0.0980 overall best weight: 0.0692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.295267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.240544 restraints weight = 7875.463| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 4.89 r_work: 0.4208 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2042 Z= 0.146 Angle : 0.529 8.229 2736 Z= 0.284 Chirality : 0.035 0.135 296 Planarity : 0.004 0.039 344 Dihedral : 4.033 19.393 260 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.45 % Allowed : 12.22 % Favored : 87.33 % 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: 2.11 (0.56), residues: 232 helix: 2.74 (0.51), residues: 112 sheet: 0.89 (0.77), residues: 38 loop : -0.26 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 PHE 0.013 0.001 PHE g 620 TYR 0.005 0.001 TYR g 485 ARG 0.001 0.000 ARG g 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8174 (mt) cc_final: 0.7920 (mm) REVERT: g 549 ASN cc_start: 0.7840 (p0) cc_final: 0.7470 (p0) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 1.7293 time to fit residues: 62.3829 Evaluate side-chains 34 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 3 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.0980 overall best weight: 0.1176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.294924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.259949 restraints weight = 7790.655| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 2.32 r_work: 0.4251 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2042 Z= 0.169 Angle : 0.553 8.207 2736 Z= 0.297 Chirality : 0.036 0.135 296 Planarity : 0.004 0.039 344 Dihedral : 4.040 21.628 260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 11.76 % Favored : 87.33 % 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 (0.55), residues: 232 helix: 2.71 (0.51), residues: 112 sheet: 1.05 (0.77), residues: 38 loop : -0.22 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 584 PHE 0.014 0.001 PHE g 620 TYR 0.007 0.001 TYR g 485 ARG 0.001 0.000 ARG g 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8243 (mt) cc_final: 0.7977 (mm) outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 1.8023 time to fit residues: 66.7185 Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0670 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.1980 chunk 7 optimal weight: 0.1980 chunk 23 optimal weight: 0.0040 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.1330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.294180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.252633 restraints weight = 7763.520| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.54 r_work: 0.4217 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2042 Z= 0.185 Angle : 0.572 8.947 2736 Z= 0.306 Chirality : 0.036 0.137 296 Planarity : 0.004 0.040 344 Dihedral : 4.049 22.296 260 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.90 % Allowed : 11.76 % Favored : 87.33 % 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: 2.21 (0.55), residues: 232 helix: 2.70 (0.50), residues: 112 sheet: 1.16 (0.76), residues: 38 loop : -0.14 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 584 PHE 0.014 0.001 PHE g 620 TYR 0.007 0.001 TYR g 485 ARG 0.001 0.000 ARG g 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8231 (mt) cc_final: 0.7936 (mm) REVERT: g 491 GLU cc_start: 0.4892 (tm-30) cc_final: 0.4536 (tt0) REVERT: g 590 ASN cc_start: 0.6055 (m-40) cc_final: 0.5771 (m110) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 2.1152 time to fit residues: 80.6982 Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.0060 chunk 5 optimal weight: 0.0980 chunk 2 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.1012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.295458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.254114 restraints weight = 7810.780| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 2.53 r_work: 0.4228 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2042 Z= 0.167 Angle : 0.567 10.091 2736 Z= 0.300 Chirality : 0.036 0.137 296 Planarity : 0.004 0.040 344 Dihedral : 4.014 21.915 260 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.45 % Allowed : 12.22 % Favored : 87.33 % 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: 2.39 (0.56), residues: 232 helix: 2.88 (0.50), residues: 112 sheet: 1.21 (0.77), residues: 38 loop : -0.07 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 584 PHE 0.013 0.001 PHE g 620 TYR 0.006 0.001 TYR g 485 ARG 0.001 0.000 ARG g 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 464 Ramachandran restraints generated. 232 Oldfield, 0 Emsley, 232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 491 GLU cc_start: 0.4756 (tm-30) cc_final: 0.4407 (tt0) REVERT: g 590 ASN cc_start: 0.6006 (m-40) cc_final: 0.5741 (m110) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 1.6395 time to fit residues: 60.8483 Evaluate side-chains 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.293923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.251373 restraints weight = 7794.893| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.78 r_work: 0.4183 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4082 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2042 Z= 0.282 Angle : 0.650 9.963 2736 Z= 0.351 Chirality : 0.039 0.176 296 Planarity : 0.006 0.066 344 Dihedral : 4.225 25.938 260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.45 % Allowed : 13.12 % Favored : 86.43 % 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: 1.88 (0.55), residues: 232 helix: 2.38 (0.51), residues: 110 sheet: 1.28 (0.77), residues: 38 loop : -0.30 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 542 HIS 0.004 0.002 HIS g 367 PHE 0.014 0.002 PHE g 620 TYR 0.011 0.001 TYR g 485 ARG 0.005 0.001 ARG g 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6552.44 seconds wall clock time: 115 minutes 1.72 seconds (6901.72 seconds total)