Starting phenix.real_space_refine on Wed Sep 17 04:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_45371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_45371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_45371.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_45371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9u_45371/09_2025/9c9u_45371.cif" } 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-2.0-5805/lib/python3.9/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: 0.64, per 1000 atoms: 0.21 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: 0.31 Conformation dependent library (CDL) restraints added in 49.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 0.36 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: 1.690 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 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:1.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 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 aren 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 covalent geometry : bond 0.01128 ( 3114) covalent geometry : angle 1.48255 ( 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 : 0.006 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: 0.0268 time to fit residues: 0.1741 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 : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1969 time to fit residues: 1.3960 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 : 0.005 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: 0.0327 time to fit residues: 0.1423 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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.7197 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 aren 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 covalent geometry : bond 0.00263 ( 3114) covalent geometry : angle 0.94159 ( 4176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 330 Ramachandran restraints generated. 165 Oldfield, 0 Emsley, 165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 330 Ramachandran restraints generated. 165 Oldfield, 0 Emsley, 165 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: 0.0972 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 : 0.003 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 : 0.005 Fit side-chains REVERT: I 22 ARG cc_start: 0.7664 (mmp80) cc_final: 0.6807 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.1723 time to fit residues: 1.0519 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 : 0.009 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 : 0.006 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: 0.0699 time to fit residues: 0.4369 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: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.079781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061910 restraints weight = 659.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.062786 restraints weight = 443.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.063269 restraints weight = 342.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063552 restraints weight = 292.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063701 restraints weight = 268.378| |-----------------------------------------------------------------------------| r_work (final): 0.3394 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.089727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068095 restraints weight = 569.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.068377 restraints weight = 468.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068506 restraints weight = 440.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068506 restraints weight = 426.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068506 restraints weight = 426.470| |-----------------------------------------------------------------------------| r_work (final): 0.3440 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067140 restraints weight = 517.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068502 restraints weight = 330.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.069108 restraints weight = 245.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.069582 restraints weight = 205.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.069858 restraints weight = 179.637| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 3114 Z= 0.132 Angle : 0.900 5.108 4176 Z= 0.396 Chirality : 0.083 0.212 438 Planarity : 0.007 0.053 522 Dihedral : 15.295 77.747 540 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.45), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.35), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.003 0.001 TYR O 22 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3114) covalent geometry : angle 0.90029 ( 4176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 Fit side-chains REVERT: G 23 ASP cc_start: 0.7766 (m-30) cc_final: 0.7482 (t0) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0152 time to fit residues: 0.0883 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 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: 0.7718 (mmp80) cc_final: 0.6651 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2039 time to fit residues: 0.8330 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 : 0.008 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: C 10 MET cc_start: 0.8188 (tpt) cc_final: 0.7905 (tpp) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0260 time to fit residues: 0.1446 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: 3.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056918 restraints weight = 656.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057852 restraints weight = 427.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058689 restraints weight = 329.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059171 restraints weight = 269.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.059269 restraints weight = 236.916| |-----------------------------------------------------------------------------| r_work (final): 0.3267 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.084300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061812 restraints weight = 866.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062275 restraints weight = 681.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062426 restraints weight = 599.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062561 restraints weight = 569.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.062567 restraints weight = 553.410| |-----------------------------------------------------------------------------| r_work (final): 0.3329 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.083059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.063609 restraints weight = 447.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064704 restraints weight = 278.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065105 restraints weight = 211.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065105 restraints weight = 185.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065105 restraints weight = 185.674| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3114 Z= 0.232 Angle : 1.055 7.700 4176 Z= 0.448 Chirality : 0.089 0.234 438 Planarity : 0.009 0.069 522 Dihedral : 14.970 80.577 540 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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 aren not related in a simple way. whole: -3.12 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 16 TYR 0.006 0.002 TYR N 22 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3114) covalent geometry : angle 1.05524 ( 4176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 264 Ramachandran restraints generated. 132 Oldfield, 0 Emsley, 132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 264 Ramachandran restraints generated. 132 Oldfield, 0 Emsley, 132 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 REVERT: A 23 ASP cc_start: 0.7944 (m-30) cc_final: 0.7671 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0135 time to fit residues: 0.0664 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 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 19 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6710 (ptm-80) REVERT: M 22 ARG cc_start: 0.8017 (mmp80) cc_final: 0.7000 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2108 time to fit residues: 0.8596 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 : 0.008 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: 0.7703 (t0) cc_final: 0.7472 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0241 time to fit residues: 0.1094 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: 0.4980 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.073151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057027 restraints weight = 756.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.058179 restraints weight = 493.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058894 restraints weight = 365.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059162 restraints weight = 299.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059513 restraints weight = 274.997| |-----------------------------------------------------------------------------| r_work (final): 0.3260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.088894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.067212 restraints weight = 604.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067664 restraints weight = 473.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067771 restraints weight = 429.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067774 restraints weight = 415.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.067815 restraints weight = 415.754| |-----------------------------------------------------------------------------| r_work (final): 0.3374 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.085245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065774 restraints weight = 526.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065282 restraints weight = 680.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064622 restraints weight = 825.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064622 restraints weight = 911.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064622 restraints weight = 911.669| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3114 Z= 0.231 Angle : 1.055 7.701 4176 Z= 0.447 Chirality : 0.089 0.232 438 Planarity : 0.009 0.068 522 Dihedral : 14.972 80.577 540 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 31.51 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 aren not related in a simple way. whole: -3.12 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 16 TYR 0.006 0.002 TYR N 22 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3114) covalent geometry : angle 1.05468 ( 4176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 264 Ramachandran restraints generated. 132 Oldfield, 0 Emsley, 132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 264 Ramachandran restraints generated. 132 Oldfield, 0 Emsley, 132 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: A 23 ASP cc_start: 0.7968 (m-30) cc_final: 0.7678 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0121 time to fit residues: 0.0594 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 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 19 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6740 (ptm-80) REVERT: M 22 ARG cc_start: 0.7934 (mmp80) cc_final: 0.6967 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2316 time to fit residues: 0.9427 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 : 0.008 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: 0.0242 time to fit residues: 0.1095 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: 0.0060 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055634 restraints weight = 538.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056971 restraints weight = 344.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057904 restraints weight = 240.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058416 restraints weight = 182.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058756 restraints weight = 153.580| |-----------------------------------------------------------------------------| r_work (final): 0.3226 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.088727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.067477 restraints weight = 614.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.068266 restraints weight = 401.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068584 restraints weight = 329.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.068689 restraints weight = 306.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.068689 restraints weight = 297.899| |-----------------------------------------------------------------------------| r_work (final): 0.3395 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.085516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064529 restraints weight = 664.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.065229 restraints weight = 518.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065487 restraints weight = 455.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065489 restraints weight = 432.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065851 restraints weight = 432.211| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 3114 Z= 0.239 Angle : 1.056 7.706 4176 Z= 0.446 Chirality : 0.088 0.228 438 Planarity : 0.009 0.067 522 Dihedral : 14.985 80.565 540 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 31.68 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 aren not related in a simple way. whole: -3.12 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 16 TYR 0.005 0.002 TYR N 22 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 3114) covalent geometry : angle 1.05566 ( 4176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 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 23 ASP cc_start: 0.7716 (m-30) cc_final: 0.7351 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0138 time to fit residues: 0.0670 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 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 19 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6723 (ptm-80) REVERT: M 22 ARG cc_start: 0.7932 (mmp80) cc_final: 0.6966 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2377 time to fit residues: 0.9696 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 : 0.020 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 : 0.005 Fit side-chains REVERT: Q 23 ASP cc_start: 0.8096 (t0) cc_final: 0.7873 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0238 time to fit residues: 0.1072 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 : 0.005 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 1 optimal weight: 0.0270 chunk 7 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056597 restraints weight = 583.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058378 restraints weight = 332.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.059452 restraints weight = 210.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060129 restraints weight = 154.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060469 restraints weight = 126.964| |-----------------------------------------------------------------------------| r_work (final): 0.3313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.085902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067449 restraints weight = 651.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067223 restraints weight = 745.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067223 restraints weight = 791.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067223 restraints weight = 791.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067223 restraints weight = 791.173| |-----------------------------------------------------------------------------| r_work (final): 0.3366 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.083440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063033 restraints weight = 538.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.063838 restraints weight = 362.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064213 restraints weight = 296.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064519 restraints weight = 272.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064519 restraints weight = 258.968| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.7114 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= 0.127 Angle : 0.920 7.403 4176 Z= 0.395 Chirality : 0.081 0.207 438 Planarity : 0.008 0.060 522 Dihedral : 14.400 78.675 540 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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 aren not related in a simple way. whole: -3.06 (0.43), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.33), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 16 TYR 0.004 0.001 TYR N 22 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3114) covalent geometry : angle 0.92039 ( 4176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 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: 0.0658 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: M 22 ARG cc_start: 0.8090 (mmp80) cc_final: 0.7041 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.2281 time to fit residues: 1.1574 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 : 0.008 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 : 0.004 Fit side-chains REVERT: N 23 ASP cc_start: 0.8170 (t0) cc_final: 0.7956 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0237 time to fit residues: 0.1063 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054996 restraints weight = 640.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055904 restraints weight = 404.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056423 restraints weight = 299.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056423 restraints weight = 250.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056423 restraints weight = 250.131| |-----------------------------------------------------------------------------| r_work (final): 0.3226 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.083262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.064584 restraints weight = 723.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064727 restraints weight = 612.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064918 restraints weight = 581.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064918 restraints weight = 556.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064918 restraints weight = 556.739| |-----------------------------------------------------------------------------| r_work (final): 0.3416 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.086423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064846 restraints weight = 482.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065635 restraints weight = 311.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066295 restraints weight = 249.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066364 restraints weight = 215.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066621 restraints weight = 211.393| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3114 Z= 0.247 Angle : 1.106 7.401 4176 Z= 0.477 Chirality : 0.091 0.295 438 Planarity : 0.010 0.065 522 Dihedral : 15.208 80.901 540 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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 aren not related in a simple way. whole: -3.25 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 16 TYR 0.007 0.003 TYR Q 22 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 3114) covalent geometry : angle 1.10609 ( 4176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 224 Ramachandran restraints generated. 112 Oldfield, 0 Emsley, 112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 224 Ramachandran restraints generated. 112 Oldfield, 0 Emsley, 112 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: 0.0086 time to fit residues: 0.0414 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 22 ARG cc_start: 0.7818 (mmp80) cc_final: 0.7079 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.1885 time to fit residues: 0.9593 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 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: 0.7481 (t0) cc_final: 0.7177 (t0) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0252 time to fit residues: 0.1397 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 : 0.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.9594 > 50: distance: 9 - 10: 3.334 distance: 10 - 16: 4.638 distance: 13 - 15: 3.724 distance: 16 - 17: 11.738 distance: 17 - 18: 20.340 distance: 18 - 19: 14.105 distance: 18 - 20: 12.460 distance: 20 - 21: 24.788 distance: 21 - 22: 10.737 distance: 21 - 24: 37.485 distance: 22 - 23: 22.280 distance: 22 - 27: 22.718 distance: 24 - 25: 19.107 distance: 24 - 26: 14.889 distance: 27 - 28: 10.131 distance: 27 - 33: 16.202 distance: 28 - 29: 16.204 distance: 28 - 31: 18.712 distance: 29 - 30: 22.654 distance: 29 - 35: 8.634 distance: 31 - 32: 14.043 distance: 32 - 33: 24.540 distance: 32 - 34: 14.377 distance: 35 - 36: 24.985 distance: 36 - 37: 14.592 distance: 37 - 38: 20.827 distance: 37 - 39: 23.092 distance: 39 - 40: 17.596 distance: 39 - 45: 3.568 distance: 40 - 41: 32.074 distance: 40 - 43: 12.788 distance: 41 - 42: 34.887 distance: 41 - 46: 20.850 distance: 43 - 44: 15.554 distance: 44 - 45: 17.013 distance: 46 - 47: 28.959 distance: 47 - 48: 28.839 distance: 47 - 50: 17.485 distance: 48 - 49: 13.396 distance: 48 - 54: 28.388 distance: 50 - 51: 31.521 distance: 51 - 52: 37.923 distance: 51 - 53: 28.313 distance: 54 - 55: 14.705 distance: 55 - 56: 31.625 distance: 56 - 57: 23.067 distance: 56 - 58: 35.701 distance: 58 - 59: 21.215 distance: 59 - 60: 12.871 distance: 59 - 62: 18.630 distance: 60 - 61: 8.555 distance: 60 - 67: 8.481 distance: 62 - 63: 11.441 distance: 63 - 64: 7.652 distance: 64 - 65: 15.641 distance: 64 - 66: 11.582 distance: 67 - 68: 7.371 distance: 67 - 73: 6.978 distance: 68 - 69: 7.335 distance: 68 - 71: 7.263 distance: 69 - 70: 5.411 distance: 69 - 75: 5.201 distance: 72 - 73: 4.010