Starting phenix.real_space_refine on Wed Jul 1 23:15:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9u_45371/07_2026/9c9u_45371.map" } resolution = 4.5 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= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1296 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1824 2.51 5 N 558 2.21 5 O 630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 158 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'HYP:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 179 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 166 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'HYP:plan-1': 5} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 0.67, per 1000 atoms: 0.22 Number of scatterers: 3018 At special positions: 0 Unit cell: (60.3, 57.62, 92.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 630 8.00 N 558 7.00 C 1824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 57.3 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1038 1.34 - 1.46: 449 1.46 - 1.57: 1555 1.57 - 1.69: 60 1.69 - 1.80: 12 Bond restraints: 3114 Sorted by residual: bond pdb=" CA HYP E 29 " pdb=" C HYP E 29 " ideal model delta sigma weight residual 1.525 1.584 -0.059 2.10e-02 2.27e+03 7.85e+00 bond pdb=" CA HYP O 14 " pdb=" C HYP O 14 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.71e+00 bond pdb=" CA HYP D 29 " pdb=" C HYP D 29 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.71e+00 bond pdb=" CA HYP P 14 " pdb=" C HYP P 14 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.70e+00 bond pdb=" CA HYP R 14 " pdb=" C HYP R 14 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.64e+00 ... (remaining 3109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 3444 1.46 - 2.91: 470 2.91 - 4.37: 101 4.37 - 5.82: 133 5.82 - 7.28: 28 Bond angle restraints: 4176 Sorted by residual: angle pdb=" N HYP H 17 " pdb=" CA HYP H 17 " pdb=" CB HYP H 17 " ideal model delta sigma weight residual 103.00 108.48 -5.48 1.10e+00 8.26e-01 2.48e+01 angle pdb=" N HYP D 17 " pdb=" CA HYP D 17 " pdb=" CB HYP D 17 " ideal model delta sigma weight residual 103.00 108.47 -5.47 1.10e+00 8.26e-01 2.47e+01 angle pdb=" N HYP F 17 " pdb=" CA HYP F 17 " pdb=" CB HYP F 17 " ideal model delta sigma weight residual 103.00 108.46 -5.46 1.10e+00 8.26e-01 2.46e+01 angle pdb=" N HYP A 17 " pdb=" CA HYP A 17 " pdb=" CB HYP A 17 " ideal model delta sigma weight residual 103.00 108.45 -5.45 1.10e+00 8.26e-01 2.45e+01 angle pdb=" N HYP E 17 " pdb=" CA HYP E 17 " pdb=" CB HYP E 17 " ideal model delta sigma weight residual 103.00 108.42 -5.42 1.10e+00 8.26e-01 2.42e+01 ... (remaining 4171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.02: 1332 12.02 - 24.04: 198 24.04 - 36.06: 96 36.06 - 48.08: 24 48.08 - 60.10: 24 Dihedral angle restraints: 1674 sinusoidal: 642 harmonic: 1032 Sorted by residual: dihedral pdb=" CA GLN J 28 " pdb=" C GLN J 28 " pdb=" N GLY J 29 " pdb=" CA GLY J 29 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLN I 28 " pdb=" C GLN I 28 " pdb=" N GLY I 29 " pdb=" CA GLY I 29 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLN L 28 " pdb=" C GLN L 28 " pdb=" N GLY L 29 " pdb=" CA GLY L 29 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 1671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 190 0.031 - 0.062: 53 0.062 - 0.093: 77 0.093 - 0.124: 89 0.124 - 0.155: 29 Chirality restraints: 438 Sorted by residual: chirality pdb=" CG HYP H 29 " pdb=" CB HYP H 29 " pdb=" CD HYP H 29 " pdb=" OD1 HYP H 29 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CG HYP E 29 " pdb=" CB HYP E 29 " pdb=" CD HYP E 29 " pdb=" OD1 HYP E 29 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CG HYP G 29 " pdb=" CB HYP G 29 " pdb=" CD HYP G 29 " pdb=" OD1 HYP G 29 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 435 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 6 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO I 7 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO I 7 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 7 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 6 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO J 7 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO J 7 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 7 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 6 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 7 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.021 5.00e-02 4.00e+02 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 72 2.62 - 3.19: 2701 3.19 - 3.76: 4869 3.76 - 4.33: 6427 4.33 - 4.90: 9838 Nonbonded interactions: 23907 Sorted by model distance: nonbonded pdb=" OE1 GLN G 25 " pdb=" OD1 HYP L 23 " model vdw 2.048 3.040 nonbonded pdb=" O GLY A 12 " pdb=" OD1 HYP R 11 " model vdw 2.111 3.040 nonbonded pdb=" OD1 HYP P 11 " pdb=" O GLY G 12 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP C 20 " pdb=" OH TYR N 22 " model vdw 2.139 3.040 nonbonded pdb=" OD2 ASP P 20 " pdb=" OH TYR Q 22 " model vdw 2.158 3.040 ... (remaining 23902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 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 : 0.011 0.059 3114 Z= 0.564 Angle : 1.483 7.276 4176 Z= 0.926 Chirality : 0.071 0.155 438 Planarity : 0.007 0.039 522 Dihedral : 15.515 60.103 1074 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: -3.13 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 16 TYR 0.019 0.005 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.01128 / 0.56 ( 3114) covalent geometry : angle 1.48255 / 0.93 ( 4176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.005 Fit side-chains REVERT: A 23 ASP cc_start: 0.8217 (m-30) cc_final: 0.7033 (t70) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0241 time to fit residues: 0.1581 Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.005 Evaluate side-chains 7 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2006 time to fit residues: 1.4239 Evaluate side-chains 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains REVERT: C 10 MET cc_start: 0.7965 (tpt) cc_final: 0.7728 (tpp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0291 time to fit residues: 0.1293 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 0.0170 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.077672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.060858 restraints weight = 640.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.061707 restraints weight = 404.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.062129 restraints weight = 310.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062534 restraints weight = 270.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062534 restraints weight = 245.397| |-----------------------------------------------------------------------------| r_work (final): 0.3318 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.084191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063351 restraints weight = 703.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064173 restraints weight = 464.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064537 restraints weight = 366.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064537 restraints weight = 330.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064537 restraints weight = 330.179| |-----------------------------------------------------------------------------| r_work (final): 0.3361 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.084227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.065679 restraints weight = 451.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.066904 restraints weight = 306.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067662 restraints weight = 247.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.067860 restraints weight = 218.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068107 restraints weight = 208.471| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.117 Angle : 0.942 5.188 4176 Z= 0.410 Chirality : 0.080 0.198 438 Planarity : 0.005 0.040 522 Dihedral : 15.661 73.588 540 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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 are not related in a simple way. whole: -2.67 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 20 TYR 0.002 0.001 TYR Q 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 3114) covalent geometry : angle 0.94159 / 0.41 ( 4176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.005 Fit side-chains REVERT: G 16 ILE cc_start: 0.9229 (mt) cc_final: 0.9018 (tt) REVERT: G 23 ASP cc_start: 0.8104 (m-30) cc_final: 0.7643 (t0) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0139 time to fit residues: 0.0968 Evaluate side-chains 5 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.005 Evaluate side-chains 6 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.008 Fit side-chains REVERT: I 22 ARG cc_start: 0.7664 (mmp80) cc_final: 0.6808 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1657 time to fit residues: 1.0131 Evaluate side-chains 2 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.007 Evaluate side-chains 6 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.005 Fit side-chains REVERT: Q 23 ASP cc_start: 0.8076 (t0) cc_final: 0.7842 (t0) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0588 time to fit residues: 0.3674 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.075312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061241 restraints weight = 572.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062191 restraints weight = 315.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063001 restraints weight = 224.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063420 restraints weight = 174.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.063545 restraints weight = 152.685| |-----------------------------------------------------------------------------| r_work (final): 0.3371 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.088260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.069453 restraints weight = 714.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069046 restraints weight = 968.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068636 restraints weight = 1117.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068636 restraints weight = 1219.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068636 restraints weight = 1219.697| |-----------------------------------------------------------------------------| r_work (final): 0.3378 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067117 restraints weight = 487.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.068032 restraints weight = 288.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068519 restraints weight = 216.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.068694 restraints weight = 183.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068801 restraints weight = 171.633| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 3114 Z= 0.167 Angle : 0.949 4.948 4176 Z= 0.417 Chirality : 0.084 0.201 438 Planarity : 0.006 0.035 522 Dihedral : 15.692 78.596 540 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % 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 are not related in a simple way. whole: -2.28 (0.45), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 19 TYR 0.003 0.001 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 3114) covalent geometry : angle 0.94941 / 0.42 ( 4176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0173 time to fit residues: 0.0444 Evaluate side-chains 1 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.005 Evaluate side-chains 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.008 Fit side-chains REVERT: M 22 ARG cc_start: 0.7701 (mmp80) cc_final: 0.6553 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1772 time to fit residues: 0.7250 Evaluate side-chains 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.007 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0243 time to fit residues: 0.0841 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 14 optimal weight: 0.0020 chunk 5 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054647 restraints weight = 540.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055715 restraints weight = 348.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.056439 restraints weight = 258.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056689 restraints weight = 203.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057021 restraints weight = 184.234| |-----------------------------------------------------------------------------| r_work (final): 0.3207 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.086590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071136 restraints weight = 703.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071003 restraints weight = 906.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071002 restraints weight = 953.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071002 restraints weight = 953.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071002 restraints weight = 953.382| |-----------------------------------------------------------------------------| r_work (final): 0.3510 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.084919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064466 restraints weight = 477.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065609 restraints weight = 276.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065969 restraints weight = 213.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065969 restraints weight = 195.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065969 restraints weight = 195.181| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3114 Z= 0.100 Angle : 0.825 4.439 4176 Z= 0.362 Chirality : 0.077 0.185 438 Planarity : 0.005 0.038 522 Dihedral : 14.319 76.889 540 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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 are not related in a simple way. whole: -2.37 (0.44), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 19 TYR 0.002 0.001 TYR C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 3114) covalent geometry : angle 0.82548 / 0.36 ( 4176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.005 Fit side-chains REVERT: F 16 ILE cc_start: 0.8839 (tp) cc_final: 0.8626 (tp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0139 time to fit residues: 0.0673 Evaluate side-chains 3 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 Evaluate side-chains 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.005 Fit side-chains REVERT: L 22 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6798 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1502 time to fit residues: 0.6128 Evaluate side-chains 2 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.007 Evaluate side-chains 5 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0266 time to fit residues: 0.1464 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054962 restraints weight = 770.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056040 restraints weight = 482.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056606 restraints weight = 355.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057231 restraints weight = 299.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057648 restraints weight = 253.271| |-----------------------------------------------------------------------------| r_work (final): 0.3199 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.085703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062920 restraints weight = 727.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062928 restraints weight = 660.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062928 restraints weight = 657.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062928 restraints weight = 657.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062928 restraints weight = 657.825| |-----------------------------------------------------------------------------| r_work (final): 0.3240 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.079821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061858 restraints weight = 478.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062479 restraints weight = 322.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062670 restraints weight = 265.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062929 restraints weight = 248.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062930 restraints weight = 231.596| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 3114 Z= 0.119 Angle : 0.843 4.902 4176 Z= 0.367 Chirality : 0.080 0.188 438 Planarity : 0.005 0.032 522 Dihedral : 15.029 79.841 540 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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 are not related in a simple way. whole: -2.31 (0.46), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 16 TYR 0.003 0.002 TYR P 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 3114) covalent geometry : angle 0.84291 / 0.37 ( 4176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Fit side-chains REVERT: F 16 ILE cc_start: 0.8860 (tp) cc_final: 0.8630 (tp) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0142 time to fit residues: 0.0541 Evaluate side-chains 3 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.009 Fit side-chains REVERT: J 19 ARG cc_start: 0.6864 (mtt180) cc_final: 0.6390 (ptm-80) REVERT: J 22 ARG cc_start: 0.7988 (mmp80) cc_final: 0.7306 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2682 time to fit residues: 1.3622 Evaluate side-chains 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.009 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0296 time to fit residues: 0.1340 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.0270 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052566 restraints weight = 687.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053369 restraints weight = 389.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053847 restraints weight = 278.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053847 restraints weight = 229.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053847 restraints weight = 229.726| |-----------------------------------------------------------------------------| r_work (final): 0.3148 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.072292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058810 restraints weight = 1081.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058959 restraints weight = 968.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058959 restraints weight = 907.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058959 restraints weight = 907.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058959 restraints weight = 907.040| |-----------------------------------------------------------------------------| r_work (final): 0.3210 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.087610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.065800 restraints weight = 498.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066520 restraints weight = 319.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066521 restraints weight = 256.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066521 restraints weight = 256.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066521 restraints weight = 256.787| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3114 Z= 0.215 Angle : 1.017 7.150 4176 Z= 0.434 Chirality : 0.088 0.216 438 Planarity : 0.008 0.040 522 Dihedral : 15.659 80.953 540 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: -2.62 (0.46), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.35), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.004 0.002 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 ( 3114) covalent geometry : angle 1.01727 / 0.43 ( 4176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0164 time to fit residues: 0.0780 Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.009 Fit side-chains REVERT: L 19 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6877 (ptm-80) REVERT: L 22 ARG cc_start: 0.8136 (mmp80) cc_final: 0.7438 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2050 time to fit residues: 1.0432 Evaluate side-chains 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Evaluate side-chains 5 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.006 Fit side-chains REVERT: N 23 ASP cc_start: 0.7474 (t0) cc_final: 0.7204 (t0) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0233 time to fit residues: 0.1283 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 7 optimal weight: 0.0020 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.0020 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054345 restraints weight = 867.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055475 restraints weight = 573.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056144 restraints weight = 402.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056567 restraints weight = 312.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056567 restraints weight = 263.313| |-----------------------------------------------------------------------------| r_work (final): 0.3184 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.079348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061633 restraints weight = 840.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062064 restraints weight = 636.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062068 restraints weight = 553.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062068 restraints weight = 552.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062068 restraints weight = 552.432| |-----------------------------------------------------------------------------| r_work (final): 0.3301 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059813 restraints weight = 538.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060414 restraints weight = 330.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060471 restraints weight = 266.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060681 restraints weight = 261.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060737 restraints weight = 245.293| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.8773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 3114 Z= 0.129 Angle : 0.871 3.960 4176 Z= 0.379 Chirality : 0.080 0.197 438 Planarity : 0.005 0.033 522 Dihedral : 15.107 80.109 540 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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 are not related in a simple way. whole: -2.56 (0.47), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 22 TYR 0.012 0.003 TYR R 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 3114) covalent geometry : angle 0.87103 / 0.38 ( 4176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0135 time to fit residues: 0.0653 Evaluate side-chains 3 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.008 Fit side-chains REVERT: B 19 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7339 (ptt90) REVERT: B 22 ARG cc_start: 0.8139 (mmp80) cc_final: 0.7520 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1916 time to fit residues: 0.9753 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.009 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0244 time to fit residues: 0.1106 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051763 restraints weight = 846.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052190 restraints weight = 561.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052328 restraints weight = 448.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.052718 restraints weight = 417.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.052771 restraints weight = 360.945| |-----------------------------------------------------------------------------| r_work (final): 0.3116 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.077043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059368 restraints weight = 886.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059370 restraints weight = 771.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059370 restraints weight = 769.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059370 restraints weight = 769.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059370 restraints weight = 769.513| |-----------------------------------------------------------------------------| r_work (final): 0.3190 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.089194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067852 restraints weight = 652.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067924 restraints weight = 571.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067924 restraints weight = 559.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067924 restraints weight = 559.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067924 restraints weight = 559.919| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.9765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3114 Z= 0.248 Angle : 1.104 6.983 4176 Z= 0.470 Chirality : 0.092 0.223 438 Planarity : 0.006 0.031 522 Dihedral : 15.906 83.404 540 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.12 % Allowed : 3.12 % Favored : 93.75 % 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 are not related in a simple way. whole: -2.63 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.37), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 16 TYR 0.018 0.005 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.25 ( 3114) covalent geometry : angle 1.10363 / 0.47 ( 4176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.005 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.0233 time to fit residues: 0.1055 Evaluate side-chains 3 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.005 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.008 Fit side-chains REVERT: B 19 ARG cc_start: 0.7596 (mtt180) cc_final: 0.6767 (ptt180) REVERT: B 22 ARG cc_start: 0.8612 (mmp80) cc_final: 0.7583 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2146 time to fit residues: 1.0911 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.008 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0249 time to fit residues: 0.1131 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051703 restraints weight = 862.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052467 restraints weight = 564.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052796 restraints weight = 422.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053110 restraints weight = 361.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053392 restraints weight = 314.863| |-----------------------------------------------------------------------------| r_work (final): 0.3137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.078331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059266 restraints weight = 815.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059459 restraints weight = 707.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059654 restraints weight = 656.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059654 restraints weight = 626.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059654 restraints weight = 626.251| |-----------------------------------------------------------------------------| r_work (final): 0.3206 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.088422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068674 restraints weight = 482.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068891 restraints weight = 398.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068891 restraints weight = 371.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068891 restraints weight = 371.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068891 restraints weight = 371.623| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 1.0074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 3114 Z= 0.187 Angle : 1.004 5.767 4176 Z= 0.430 Chirality : 0.087 0.209 438 Planarity : 0.006 0.031 522 Dihedral : 15.519 81.013 540 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: -2.54 (0.49), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 22 TYR 0.015 0.004 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 ( 3114) covalent geometry : angle 1.00434 / 0.43 ( 4176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0079 time to fit residues: 0.0391 Evaluate side-chains 4 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.003 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.005 Fit side-chains REVERT: B 19 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6749 (ptt180) REVERT: B 22 ARG cc_start: 0.8555 (mmp80) cc_final: 0.7473 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1697 time to fit residues: 0.8605 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.008 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains REVERT: N 23 ASP cc_start: 0.7200 (t0) cc_final: 0.6975 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0266 time to fit residues: 0.1196 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047236 restraints weight = 1071.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048092 restraints weight = 721.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048461 restraints weight = 566.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048696 restraints weight = 505.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048697 restraints weight = 471.446| |-----------------------------------------------------------------------------| r_work (final): 0.3016 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053463 restraints weight = 939.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053585 restraints weight = 825.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053585 restraints weight = 795.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053585 restraints weight = 795.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053585 restraints weight = 795.475| |-----------------------------------------------------------------------------| r_work (final): 0.3053 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.085703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066799 restraints weight = 723.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067115 restraints weight = 576.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067115 restraints weight = 527.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067115 restraints weight = 527.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067115 restraints weight = 527.791| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 1.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3114 Z= 0.295 Angle : 1.172 6.561 4176 Z= 0.504 Chirality : 0.096 0.241 438 Planarity : 0.007 0.040 522 Dihedral : 16.121 83.684 540 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: -2.58 (0.50), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 22 TYR 0.019 0.005 TYR O 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.29 ( 3114) covalent geometry : angle 1.17242 / 0.50 ( 4176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0242 time to fit residues: 0.0581 Evaluate side-chains 1 residues out of total 9 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.005 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.008 Fit side-chains REVERT: L 11 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8681 (mmmt) REVERT: L 19 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6652 (ptt180) REVERT: L 22 ARG cc_start: 0.8486 (mmp80) cc_final: 0.7457 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1595 time to fit residues: 0.8125 Evaluate side-chains 5 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 Evaluate side-chains 4 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.003 Fit side-chains REVERT: N 23 ASP cc_start: 0.7234 (t0) cc_final: 0.6993 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0159 time to fit residues: 0.0719 Evaluate side-chains 3 residues out of total 10 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044555 restraints weight = 1042.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045058 restraints weight = 818.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045260 restraints weight = 713.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045260 restraints weight = 669.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045260 restraints weight = 669.642| |-----------------------------------------------------------------------------| r_work (final): 0.2890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055802 restraints weight = 975.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055802 restraints weight = 861.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055802 restraints weight = 861.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055802 restraints weight = 861.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055802 restraints weight = 861.552| |-----------------------------------------------------------------------------| r_work (final): 0.3047 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.064404 restraints weight = 798.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064669 restraints weight = 606.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064669 restraints weight = 564.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064669 restraints weight = 564.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064669 restraints weight = 564.061| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 1.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.027 3114 Z= 0.395 Angle : 1.264 6.289 4176 Z= 0.557 Chirality : 0.100 0.278 438 Planarity : 0.008 0.044 522 Dihedral : 16.574 85.050 540 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: -2.80 (0.50), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.38), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG L 22 TYR 0.023 0.006 TYR N 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.40 ( 3114) covalent geometry : angle 1.26413 / 0.56 ( 4176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 658.45 seconds wall clock time: 12 minutes 1.28 seconds (721.28 seconds total)