Starting phenix.real_space_refine on Tue Feb 11 04:34:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz7_40902/02_2025/8sz7_40902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz7_40902/02_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_40902/02_2025/8sz7_40902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz7_40902/02_2025/8sz7_40902.map" model { file = "/net/cci-nas-00/data/ceres_data/8sz7_40902/02_2025/8sz7_40902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz7_40902/02_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-5592/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: 4.37, per 1000 atoms: 1.09 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: 1.04 Conformation dependent library (CDL) restraints added in 252.6 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: 1.25 Time building geometry restraints manager: 1.27 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: 8.220 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.020 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- 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 : 0.305 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: 2.2852 time to fit residues: 107.2732 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 : 0.343 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 23 optimal weight: 0.0970 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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 = 0.293166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.251794 restraints weight = 7876.991| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 2.60 r_work: 0.4334 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4262 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2042 Z= 0.297 Angle : 0.664 7.664 2736 Z= 0.367 Chirality : 0.041 0.145 296 Planarity : 0.005 0.040 344 Dihedral : 4.435 21.769 260 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.45 % Allowed : 7.69 % Favored : 91.86 % 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: 1.65 (0.55), residues: 232 helix: 2.39 (0.52), residues: 107 sheet: 1.08 (0.83), residues: 38 loop : -0.57 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP g 616 HIS 0.005 0.001 HIS g 367 PHE 0.017 0.002 PHE g 366 TYR 0.014 0.002 TYR g 597 ARG 0.003 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 43 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8087 (mt) cc_final: 0.7887 (mm) REVERT: g 470 ARG cc_start: 0.5847 (mtm110) cc_final: 0.5212 (mtm-85) REVERT: g 549 ASN cc_start: 0.7215 (p0) cc_final: 0.6892 (p0) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 1.3734 time to fit residues: 59.6707 Evaluate side-chains 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.0570 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 610 GLN g 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.294295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.238014 restraints weight = 7744.051| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 3.45 r_work: 0.4185 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2042 Z= 0.206 Angle : 0.574 7.526 2736 Z= 0.317 Chirality : 0.037 0.130 296 Planarity : 0.004 0.039 344 Dihedral : 4.215 17.606 260 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.45 % Allowed : 10.86 % Favored : 88.69 % 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: 1.78 (0.56), residues: 232 helix: 2.25 (0.53), residues: 110 sheet: 1.05 (0.82), residues: 38 loop : -0.18 (0.63), residues: 84 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 0.016 0.002 PHE g 620 TYR 0.012 0.001 TYR g 485 ARG 0.003 0.000 ARG g 601 *********************** 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 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8067 (mt) cc_final: 0.7831 (mm) REVERT: g 470 ARG cc_start: 0.6227 (mtm110) cc_final: 0.5541 (mtp-110) REVERT: g 549 ASN cc_start: 0.7453 (p0) cc_final: 0.7066 (p0) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 1.5911 time to fit residues: 62.4033 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 : 0.326 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.0670 chunk 20 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.0770 ------------------------------------------------------------------------------- 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 = 0.5012 r_free = 0.5012 target = 0.295207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.253288 restraints weight = 7790.985| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.43 r_work: 0.4206 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2042 Z= 0.158 Angle : 0.538 7.723 2736 Z= 0.293 Chirality : 0.037 0.138 296 Planarity : 0.004 0.035 344 Dihedral : 4.134 17.319 260 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 2.05 (0.56), residues: 232 helix: 2.48 (0.52), residues: 112 sheet: 1.02 (0.79), residues: 38 loop : -0.02 (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 0.008 0.001 PHE g 579 TYR 0.008 0.001 TYR g 485 ARG 0.001 0.000 ARG g 470 *********************** 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 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8093 (mt) cc_final: 0.7870 (mm) REVERT: g 470 ARG cc_start: 0.6424 (mtm110) cc_final: 0.5532 (mtp-110) REVERT: g 549 ASN cc_start: 0.7577 (p0) cc_final: 0.7212 (p0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 1.4321 time to fit residues: 54.8939 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.0870 chunk 2 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.1756 ------------------------------------------------------------------------------- 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 = 0.5003 r_free = 0.5003 target = 0.293880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.239306 restraints weight = 8047.942| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 4.66 r_work: 0.4192 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2042 Z= 0.217 Angle : 0.575 7.981 2736 Z= 0.315 Chirality : 0.038 0.134 296 Planarity : 0.004 0.041 344 Dihedral : 4.142 21.374 260 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.49 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: 1.83 (0.55), residues: 232 helix: 2.36 (0.51), residues: 112 sheet: 0.86 (0.78), residues: 38 loop : -0.21 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 PHE 0.009 0.001 PHE g 409 TYR 0.010 0.001 TYR g 485 ARG 0.004 0.000 ARG g 470 *********************** 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 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 420 ILE cc_start: 0.8186 (mt) cc_final: 0.7945 (mm) REVERT: g 470 ARG cc_start: 0.6656 (mtm110) cc_final: 0.5626 (mtp-110) REVERT: g 549 ASN cc_start: 0.7716 (p0) cc_final: 0.7317 (p0) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.5119 time to fit residues: 54.7054 Evaluate side-chains 32 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 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: 10.0000 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 0.0060 chunk 21 optimal weight: 0.0870 chunk 6 optimal weight: 0.0770 overall best weight: 0.0730 ------------------------------------------------------------------------------- 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 = 0.5015 r_free = 0.5015 target = 0.295107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.241745 restraints weight = 7793.094| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.39 r_work: 0.4183 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2042 Z= 0.144 Angle : 0.533 8.087 2736 Z= 0.287 Chirality : 0.036 0.134 296 Planarity : 0.004 0.039 344 Dihedral : 4.034 18.532 260 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.24 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: 2.18 (0.55), residues: 232 helix: 2.82 (0.51), residues: 112 sheet: 0.81 (0.75), residues: 38 loop : -0.21 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 542 HIS 0.004 0.001 HIS g 367 PHE 0.007 0.001 PHE g 620 TYR 0.006 0.001 TYR g 485 ARG 0.002 0.000 ARG g 470 *********************** 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 33 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.329 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: 0.8098 (mt) cc_final: 0.7867 (mm) REVERT: g 470 ARG cc_start: 0.6770 (mtm110) cc_final: 0.5556 (mtp-110) REVERT: g 549 ASN cc_start: 0.7530 (p0) cc_final: 0.7167 (p0) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 1.8426 time to fit residues: 62.7015 Evaluate side-chains 33 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0870 chunk 3 optimal weight: 0.0870 chunk 5 optimal weight: 0.0570 chunk 23 optimal weight: 0.0970 chunk 6 optimal weight: 0.0770 chunk 7 optimal weight: 0.0670 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 0.0970 chunk 21 optimal weight: 0.0870 chunk 22 optimal weight: 0.0770 overall best weight: 0.0730 ------------------------------------------------------------------------------- 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 = 0.5020 r_free = 0.5020 target = 0.295767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.254879 restraints weight = 7759.517| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 2.58 r_work: 0.4258 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4142 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.5295 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= 0.149 Angle : 0.542 8.159 2736 Z= 0.289 Chirality : 0.036 0.134 296 Planarity : 0.004 0.038 344 Dihedral : 3.945 19.332 260 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 12.67 % 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: 2.42 (0.55), residues: 232 helix: 3.08 (0.51), residues: 112 sheet: 0.88 (0.74), residues: 38 loop : -0.17 (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 0.018 0.001 PHE g 620 TYR 0.006 0.001 TYR g 485 ARG 0.002 0.000 ARG g 470 *********************** 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: 2 poor density : 33 time to evaluate : 0.329 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: 0.8118 (mt) cc_final: 0.7895 (mm) REVERT: g 470 ARG cc_start: 0.6876 (mtm110) cc_final: 0.5783 (mtp-110) REVERT: g 549 ASN cc_start: 0.7337 (p0) cc_final: 0.7023 (p0) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 1.6861 time to fit residues: 60.8438 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 : 0.376 ------------------------------------------------------------------------------- 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: 0.3980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 3 optimal weight: 0.0980 chunk 20 optimal weight: 0.0980 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.0670 overall best weight: 0.0916 ------------------------------------------------------------------------------- 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 = 0.5017 r_free = 0.5017 target = 0.295405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.241529 restraints weight = 7643.714| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 4.64 r_work: 0.4203 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2042 Z= 0.158 Angle : 0.563 8.307 2736 Z= 0.296 Chirality : 0.036 0.135 296 Planarity : 0.004 0.039 344 Dihedral : 3.917 20.128 260 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 11.31 % 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: 2.50 (0.56), residues: 232 helix: 3.11 (0.51), residues: 112 sheet: 0.96 (0.73), residues: 38 loop : -0.08 (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 0.017 0.001 PHE g 620 TYR 0.006 0.001 TYR g 485 ARG 0.003 0.000 ARG g 470 *********************** 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: 3 poor density : 33 time to evaluate : 0.343 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: 0.8134 (mt) cc_final: 0.7905 (mm) REVERT: g 470 ARG cc_start: 0.6988 (mtm110) cc_final: 0.5800 (mtp-110) REVERT: g 549 ASN cc_start: 0.7799 (p0) cc_final: 0.7432 (p0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 1.6364 time to fit residues: 60.7595 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR 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: 0.5980 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 7 optimal weight: 0.0670 chunk 23 optimal weight: 0.0870 chunk 21 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.1454 ------------------------------------------------------------------------------- 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 = 0.5004 r_free = 0.5004 target = 0.293874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.252193 restraints weight = 7838.107| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 2.55 r_work: 0.4160 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.5554 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= 0.195 Angle : 0.604 9.200 2736 Z= 0.316 Chirality : 0.036 0.135 296 Planarity : 0.004 0.038 344 Dihedral : 3.987 22.680 260 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.23 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: 2.30 (0.55), residues: 232 helix: 2.91 (0.50), residues: 112 sheet: 0.98 (0.74), residues: 38 loop : -0.18 (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 0.015 0.001 PHE g 620 TYR 0.009 0.001 TYR g 626 ARG 0.004 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 35 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.332 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: 0.8098 (mt) cc_final: 0.7836 (mm) REVERT: g 470 ARG cc_start: 0.6978 (mtm110) cc_final: 0.5904 (mtp-110) REVERT: g 549 ASN cc_start: 0.7616 (p0) cc_final: 0.7288 (p0) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.7030 time to fit residues: 61.4407 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR 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: 0.0470 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 5 optimal weight: 0.1980 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.1478 ------------------------------------------------------------------------------- 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 = 0.5010 r_free = 0.5010 target = 0.294552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.252777 restraints weight = 7846.701| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 2.54 r_work: 0.4173 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5682 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= 0.196 Angle : 0.615 9.940 2736 Z= 0.320 Chirality : 0.036 0.137 296 Planarity : 0.004 0.039 344 Dihedral : 4.013 23.191 260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.90 % Allowed : 12.22 % 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: 2.27 (0.55), residues: 232 helix: 2.79 (0.50), residues: 112 sheet: 1.05 (0.75), residues: 38 loop : -0.11 (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 0.016 0.001 TYR g 626 ARG 0.004 0.000 ARG g 470 ********************** 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 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: g 379 PHE cc_start: 0.7882 (p90) cc_final: 0.7648 (p90) REVERT: g 420 ILE cc_start: 0.8074 (mt) cc_final: 0.7779 (mm) REVERT: g 470 ARG cc_start: 0.6950 (mtm110) cc_final: 0.5841 (mtp-110) REVERT: g 491 GLU cc_start: 0.4741 (tm-30) cc_final: 0.4379 (tt0) REVERT: g 549 ASN cc_start: 0.7777 (p0) cc_final: 0.7477 (p0) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 1.6862 time to fit residues: 60.8659 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR 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: 0.0870 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 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: 3.9990 chunk 22 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 overall best weight: 0.2758 ------------------------------------------------------------------------------- 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 = 0.4998 r_free = 0.4998 target = 0.293229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.244030 restraints weight = 7784.352| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 4.71 r_work: 0.4160 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.5799 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= 0.298 Angle : 0.680 9.748 2736 Z= 0.361 Chirality : 0.040 0.165 296 Planarity : 0.005 0.043 344 Dihedral : 4.211 26.346 260 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.90 % Allowed : 12.22 % 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: 1.83 (0.55), residues: 232 helix: 2.40 (0.51), residues: 110 sheet: 1.19 (0.76), residues: 38 loop : -0.39 (0.64), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 PHE 0.014 0.002 PHE g 620 TYR 0.013 0.001 TYR g 626 ARG 0.006 0.000 ARG g 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6079.74 seconds wall clock time: 107 minutes 8.40 seconds (6428.40 seconds total)