Starting phenix.real_space_refine on Fri Aug 22 14:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz7_40902/08_2025/8sz7_40902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz7_40902/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sz7_40902/08_2025/8sz7_40902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz7_40902/08_2025/8sz7_40902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sz7_40902/08_2025/8sz7_40902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz7_40902/08_2025/8sz7_40902.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.88, per 1000 atoms: 0.22 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: 0.23 Conformation dependent library (CDL) restraints added in 53.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.07 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: 0.98 Time building geometry restraints manager: 0.33 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: 11.950 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: 0.040 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.840 Find NCS groups from input model: 0.010 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:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- 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= 0.129 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG g 678 TYR 0.009 0.001 TYR g 485 PHE 0.006 0.001 PHE g 409 TRP 0.002 0.001 TRP g 542 HIS 0.004 0.001 HIS g 490 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2042) covalent geometry : angle 0.45823 ( 2736) hydrogen bonds : bond 0.22558 ( 97) hydrogen bonds : angle 6.98097 ( 279) *********************** 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 : 0.065 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: 1.0440 time to fit residues: 48.9166 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 4 optimal weight: 0.2980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.4995 r_free = 0.4995 target = 0.292202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.251741 restraints weight = 8062.923| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.43 r_work: 0.4320 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4240 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2042 Z= 0.217 Angle : 0.687 7.559 2736 Z= 0.380 Chirality : 0.042 0.153 296 Planarity : 0.005 0.047 344 Dihedral : 4.459 21.987 260 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 1.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.55), residues: 232 helix: 2.27 (0.52), residues: 107 sheet: 1.03 (0.82), residues: 38 loop : -0.59 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG g 470 TYR 0.013 0.002 TYR g 485 PHE 0.015 0.002 PHE g 366 TRP 0.003 0.000 TRP g 616 HIS 0.005 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 2042) covalent geometry : angle 0.68698 ( 2736) hydrogen bonds : bond 0.06253 ( 97) hydrogen bonds : angle 4.98951 ( 279) *********************** 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 45 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.110 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: 0.8044 (mt) cc_final: 0.7815 (mm) REVERT: g 549 ASN cc_start: 0.7412 (p0) cc_final: 0.7095 (p0) REVERT: g 589 PHE cc_start: 0.7381 (t80) cc_final: 0.7148 (t80) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.6862 time to fit residues: 31.1639 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 : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.3980 chunk 21 optimal weight: 0.0570 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.0020 chunk 6 optimal weight: 0.0980 overall best weight: 0.0682 ------------------------------------------------------------------------------- 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 = 0.5028 r_free = 0.5028 target = 0.296237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.255043 restraints weight = 7954.135| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.44 r_work: 0.4368 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.4287 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2042 Z= 0.108 Angle : 0.528 7.580 2736 Z= 0.288 Chirality : 0.036 0.133 296 Planarity : 0.003 0.032 344 Dihedral : 4.150 16.672 260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.55), residues: 232 helix: 2.45 (0.51), residues: 111 sheet: 1.06 (0.81), residues: 38 loop : -0.19 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 601 TYR 0.009 0.001 TYR g 485 PHE 0.014 0.001 PHE g 620 TRP 0.003 0.000 TRP g 542 HIS 0.005 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 2042) covalent geometry : angle 0.52798 ( 2736) hydrogen bonds : bond 0.04948 ( 97) hydrogen bonds : angle 4.41951 ( 279) *********************** 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 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.089 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: 0.8021 (mt) cc_final: 0.7810 (mm) REVERT: g 549 ASN cc_start: 0.7403 (p0) cc_final: 0.7007 (p0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.7916 time to fit residues: 30.0381 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 : 0.135 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.0770 chunk 6 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 0 optimal weight: 0.0970 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.0870 overall best weight: 0.0912 ------------------------------------------------------------------------------- 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 = 0.294980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.251827 restraints weight = 7763.780| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 2.46 r_work: 0.4233 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4184 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= 0.108 Angle : 0.522 7.702 2736 Z= 0.285 Chirality : 0.036 0.138 296 Planarity : 0.004 0.033 344 Dihedral : 4.063 16.262 260 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.55), residues: 232 helix: 2.56 (0.51), residues: 112 sheet: 0.93 (0.79), residues: 38 loop : 0.03 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 573 TYR 0.007 0.001 TYR g 485 PHE 0.014 0.001 PHE g 620 TRP 0.004 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2042) covalent geometry : angle 0.52239 ( 2736) hydrogen bonds : bond 0.04576 ( 97) hydrogen bonds : angle 4.26363 ( 279) *********************** 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: 2 poor density : 38 time to evaluate : 0.067 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: 0.8085 (mt) cc_final: 0.7879 (mm) REVERT: g 549 ASN cc_start: 0.7424 (p0) cc_final: 0.7049 (p0) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.6938 time to fit residues: 28.4837 Evaluate side-chains 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 478 LEU 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 17 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 3 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 6 optimal weight: 0.0570 chunk 22 optimal weight: 0.1980 overall best weight: 0.1276 ------------------------------------------------------------------------------- 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 = 0.295055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.240533 restraints weight = 7921.216| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 3.58 r_work: 0.4198 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4085 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.4552 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= 0.126 Angle : 0.543 7.852 2736 Z= 0.296 Chirality : 0.037 0.138 296 Planarity : 0.004 0.035 344 Dihedral : 4.084 18.366 260 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 10.86 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.55), residues: 232 helix: 2.54 (0.51), residues: 112 sheet: 0.93 (0.77), residues: 38 loop : -0.10 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 364 TYR 0.008 0.001 TYR g 485 PHE 0.009 0.001 PHE g 620 TRP 0.004 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2042) covalent geometry : angle 0.54267 ( 2736) hydrogen bonds : bond 0.04696 ( 97) hydrogen bonds : angle 4.22864 ( 279) *********************** 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 40 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 549 ASN cc_start: 0.7558 (p0) cc_final: 0.7201 (p0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.5953 time to fit residues: 23.9446 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 478 LEU 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 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 7 optimal weight: 0.0570 chunk 20 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 8 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 overall best weight: 0.0852 ------------------------------------------------------------------------------- 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 = 0.295915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.241212 restraints weight = 7924.878| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 3.77 r_work: 0.4189 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2042 Z= 0.107 Angle : 0.524 8.016 2736 Z= 0.285 Chirality : 0.036 0.135 296 Planarity : 0.003 0.037 344 Dihedral : 4.050 18.292 260 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.55), residues: 232 helix: 2.75 (0.51), residues: 112 sheet: 0.80 (0.77), residues: 38 loop : -0.22 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 386 TYR 0.007 0.001 TYR g 626 PHE 0.008 0.001 PHE g 620 TRP 0.005 0.001 TRP g 542 HIS 0.004 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 2042) covalent geometry : angle 0.52448 ( 2736) hydrogen bonds : bond 0.04250 ( 97) hydrogen bonds : angle 4.09957 ( 279) *********************** 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 36 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 549 ASN cc_start: 0.7496 (p0) cc_final: 0.7146 (p0) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.7266 time to fit residues: 26.2373 Evaluate side-chains 33 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 478 LEU 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 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 23 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 = 0.4992 r_free = 0.4992 target = 0.292587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.250229 restraints weight = 7931.939| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 2.52 r_work: 0.4189 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4093 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2042 Z= 0.218 Angle : 0.646 8.124 2736 Z= 0.356 Chirality : 0.041 0.188 296 Planarity : 0.005 0.046 344 Dihedral : 4.275 25.064 260 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.54), residues: 232 helix: 2.48 (0.51), residues: 106 sheet: 0.79 (0.77), residues: 38 loop : -0.87 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 470 TYR 0.013 0.001 TYR g 485 PHE 0.013 0.002 PHE g 620 TRP 0.004 0.001 TRP g 542 HIS 0.004 0.002 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 2042) covalent geometry : angle 0.64632 ( 2736) hydrogen bonds : bond 0.05921 ( 97) hydrogen bonds : angle 4.25365 ( 279) *********************** 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 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.095 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 549 ASN cc_start: 0.7646 (p0) cc_final: 0.7314 (p0) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.7394 time to fit residues: 28.1148 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 : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 478 LEU 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 1 optimal weight: 0.0770 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 0.1592 ------------------------------------------------------------------------------- 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 = 0.293829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.249200 restraints weight = 7796.118| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.43 r_work: 0.4237 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.5380 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= 0.136 Angle : 0.569 8.229 2736 Z= 0.309 Chirality : 0.037 0.135 296 Planarity : 0.004 0.042 344 Dihedral : 4.151 22.392 260 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.81 % Allowed : 11.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.55), residues: 232 helix: 2.39 (0.51), residues: 110 sheet: 0.89 (0.77), residues: 38 loop : -0.51 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 470 TYR 0.009 0.001 TYR g 485 PHE 0.013 0.001 PHE g 620 TRP 0.005 0.001 TRP g 542 HIS 0.004 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2042) covalent geometry : angle 0.56851 ( 2736) hydrogen bonds : bond 0.04969 ( 97) hydrogen bonds : angle 4.13822 ( 279) *********************** 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 37 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.119 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 549 ASN cc_start: 0.7707 (p0) cc_final: 0.7361 (p0) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.6684 time to fit residues: 25.4797 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 : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 478 LEU 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 23 optimal weight: 0.0770 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 0.0570 overall best weight: 0.1034 ------------------------------------------------------------------------------- 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 = 0.5009 r_free = 0.5009 target = 0.294353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.252829 restraints weight = 7902.500| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.51 r_work: 0.4207 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4109 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.5534 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= 0.114 Angle : 0.560 9.015 2736 Z= 0.299 Chirality : 0.036 0.136 296 Planarity : 0.004 0.039 344 Dihedral : 4.103 21.830 260 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.81 % Allowed : 11.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.55), residues: 232 helix: 2.59 (0.51), residues: 112 sheet: 1.00 (0.77), residues: 38 loop : -0.24 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 386 TYR 0.007 0.001 TYR g 626 PHE 0.013 0.001 PHE g 620 TRP 0.006 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2042) covalent geometry : angle 0.55957 ( 2736) hydrogen bonds : bond 0.04458 ( 97) hydrogen bonds : angle 4.01109 ( 279) *********************** 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 38 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.121 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 549 ASN cc_start: 0.7765 (p0) cc_final: 0.7468 (p0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.7172 time to fit residues: 27.9680 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 : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 478 LEU 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 20 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 0.0870 chunk 8 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 0.1874 ------------------------------------------------------------------------------- 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 = 0.5006 r_free = 0.5006 target = 0.294282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.252509 restraints weight = 7743.625| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.40 r_work: 0.4222 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5617 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= 0.155 Angle : 0.613 9.815 2736 Z= 0.330 Chirality : 0.037 0.137 296 Planarity : 0.005 0.046 344 Dihedral : 4.181 24.256 260 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.36 % Allowed : 12.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.55), residues: 232 helix: 2.52 (0.51), residues: 110 sheet: 1.05 (0.76), residues: 38 loop : -0.39 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 470 TYR 0.016 0.001 TYR g 626 PHE 0.013 0.002 PHE g 620 TRP 0.005 0.001 TRP g 542 HIS 0.004 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 2042) covalent geometry : angle 0.61260 ( 2736) hydrogen bonds : bond 0.05091 ( 97) hydrogen bonds : angle 4.07153 ( 279) ********************** 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: 3 poor density : 33 time to evaluate : 0.073 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: 0.4921 (tm-30) cc_final: 0.4545 (tt0) REVERT: g 549 ASN cc_start: 0.7778 (p0) cc_final: 0.7483 (p0) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.6626 time to fit residues: 24.5061 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 471 THR Chi-restraints excluded: chain g residue 478 LEU 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 16 optimal weight: 5.9990 chunk 11 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 6 optimal weight: 0.0670 overall best weight: 0.1274 ------------------------------------------------------------------------------- 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 = 0.5008 r_free = 0.5008 target = 0.294388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.252860 restraints weight = 7724.002| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.40 r_work: 0.4235 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5678 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= 0.123 Angle : 0.581 9.667 2736 Z= 0.308 Chirality : 0.036 0.137 296 Planarity : 0.004 0.040 344 Dihedral : 4.149 23.041 260 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.36 % Allowed : 12.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.55), residues: 232 helix: 2.62 (0.51), residues: 112 sheet: 1.14 (0.76), residues: 38 loop : -0.15 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 470 TYR 0.013 0.001 TYR g 626 PHE 0.013 0.002 PHE g 620 TRP 0.005 0.001 TRP g 542 HIS 0.003 0.001 HIS g 367 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 2042) covalent geometry : angle 0.58096 ( 2736) hydrogen bonds : bond 0.04574 ( 97) hydrogen bonds : angle 3.99631 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.55 seconds wall clock time: 47 minutes 23.94 seconds (2843.94 seconds total)