Starting phenix.real_space_refine on Wed Mar 5 23:14:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9u_45371/03_2025/9c9u_45371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9u_45371/03_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_45371/03_2025/9c9u_45371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9u_45371/03_2025/9c9u_45371.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9u_45371/03_2025/9c9u_45371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9u_45371/03_2025/9c9u_45371.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: I, K, J, M, L, O, N, Q, P, R, E, D, G, F, H Time building chain proxies: 2.48, per 1000 atoms: 0.82 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: 0.92 Conformation dependent library (CDL) restraints added in 211.0 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: 0.51 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: 1.07 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 12.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TYR 0.019 0.005 TYR N 22 ARG 0.005 0.001 ARG I 16 *********************** 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 7 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.4585 time to fit residues: 3.2633 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 : 0.022 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 : 0.016 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: 0.0913 time to fit residues: 0.3985 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 : 0.016 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 : 0.013 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: 0.0580 time to fit residues: 0.3797 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 : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.077526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061635 restraints weight = 892.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061613 restraints weight = 930.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061616 restraints weight = 914.052| |-----------------------------------------------------------------------------| r_work (final): 0.3248 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.082901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062348 restraints weight = 579.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062828 restraints weight = 469.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062828 restraints weight = 418.597| |-----------------------------------------------------------------------------| r_work (final): 0.3285 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.072551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057087 restraints weight = 717.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057809 restraints weight = 463.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058187 restraints weight = 354.987| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 3114 Z= 0.383 Angle : 1.320 9.633 4176 Z= 0.570 Chirality : 0.102 0.248 438 Planarity : 0.010 0.049 522 Dihedral : 17.163 82.763 540 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.43), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.33), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR N 22 ARG 0.006 0.001 ARG K 22 *********************** 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 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.022 Fit side-chains REVERT: I 19 ARG cc_start: 0.6899 (mtt180) cc_final: 0.6336 (ptm-80) REVERT: I 22 ARG cc_start: 0.8272 (mmp80) cc_final: 0.7588 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.4083 time to fit residues: 2.4972 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 : 0.021 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 : 0.016 Fit side-chains REVERT: Q 23 ASP cc_start: 0.8315 (t0) cc_final: 0.8045 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0667 time to fit residues: 0.2996 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 : 0.015 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0401 time to fit residues: 0.1891 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.080391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061473 restraints weight = 798.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061809 restraints weight = 671.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061807 restraints weight = 608.116| |-----------------------------------------------------------------------------| r_work (final): 0.3243 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.081909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061623 restraints weight = 448.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.062451 restraints weight = 277.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062757 restraints weight = 208.674| |-----------------------------------------------------------------------------| r_work (final): 0.3283 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051275 restraints weight = 726.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052046 restraints weight = 464.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052519 restraints weight = 346.734| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.022 3114 Z= 0.309 Angle : 1.190 6.692 4176 Z= 0.512 Chirality : 0.097 0.253 438 Planarity : 0.010 0.062 522 Dihedral : 15.300 80.114 540 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 24.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 22 ARG 0.004 0.001 ARG L 22 *********************** 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 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.020 Fit side-chains REVERT: J 19 ARG cc_start: 0.7308 (mtt180) cc_final: 0.6179 (ptm-80) REVERT: J 22 ARG cc_start: 0.8239 (mmp80) cc_final: 0.7169 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.5300 time to fit residues: 2.1591 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 : 0.020 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 : 0.014 Fit side-chains REVERT: N 23 ASP cc_start: 0.7335 (t0) cc_final: 0.7084 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0611 time to fit residues: 0.2744 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 : 0.014 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0378 time to fit residues: 0.1370 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.074174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057911 restraints weight = 923.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057911 restraints weight = 842.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057911 restraints weight = 842.203| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.085832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063036 restraints weight = 601.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063012 restraints weight = 618.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062924 restraints weight = 622.976| |-----------------------------------------------------------------------------| r_work (final): 0.3172 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.048513 restraints weight = 796.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.049129 restraints weight = 510.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049475 restraints weight = 393.848| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.8959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3114 Z= 0.337 Angle : 1.249 8.543 4176 Z= 0.534 Chirality : 0.100 0.261 438 Planarity : 0.011 0.085 522 Dihedral : 15.636 82.344 540 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.47), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR O 22 ARG 0.005 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 4 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 4 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.023 Fit side-chains REVERT: I 19 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6236 (ptt90) REVERT: I 22 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7644 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.5358 time to fit residues: 2.1880 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 : 0.022 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 : 0.014 Fit side-chains REVERT: N 23 ASP cc_start: 0.7026 (t0) cc_final: 0.6686 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0602 time to fit residues: 0.2707 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 : 0.016 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 : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0366 time to fit residues: 0.1750 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 : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 26 optimal weight: 0.0020 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 29 optimal weight: 0.5980 overall best weight: 0.1724 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.069888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055119 restraints weight = 927.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055118 restraints weight = 890.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055118 restraints weight = 890.738| |-----------------------------------------------------------------------------| r_work (final): 0.3127 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.086299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062240 restraints weight = 630.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062239 restraints weight = 608.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062239 restraints weight = 608.376| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051421 restraints weight = 700.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052216 restraints weight = 537.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.052593 restraints weight = 439.379| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.8871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 16.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 22 ARG 0.004 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 240 Ramachandran restraints generated. 120 Oldfield, 0 Emsley, 120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.022 Fit side-chains REVERT: L 19 ARG cc_start: 0.7007 (mtt180) cc_final: 0.6368 (ptt90) REVERT: L 22 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7551 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.4564 time to fit residues: 2.3271 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 : 0.021 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 : 0.015 Fit side-chains REVERT: N 23 ASP cc_start: 0.7000 (t0) cc_final: 0.6655 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0654 time to fit residues: 0.2940 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 : 0.015 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 : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0354 time to fit residues: 0.1318 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.0040 chunk 29 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- 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 = 0.074687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058676 restraints weight = 772.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058676 restraints weight = 796.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058676 restraints weight = 796.039| |-----------------------------------------------------------------------------| r_work (final): 0.3211 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062019 restraints weight = 515.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.062504 restraints weight = 423.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062542 restraints weight = 372.262| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.061683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051418 restraints weight = 684.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052045 restraints weight = 464.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052442 restraints weight = 365.691| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.8885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 22 ARG 0.004 0.001 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 6 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 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.021 Fit side-chains REVERT: I 19 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6198 (ptt90) REVERT: I 22 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7572 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.6140 time to fit residues: 2.5007 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 : 0.021 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 : 0.016 Fit side-chains REVERT: O 10 MET cc_start: 0.8120 (tpp) cc_final: 0.7809 (tmm) REVERT: O 23 ASP cc_start: 0.7481 (t0) cc_final: 0.7176 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0687 time to fit residues: 0.3078 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 : 0.016 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0355 time to fit residues: 0.1704 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058470 restraints weight = 829.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058470 restraints weight = 859.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058470 restraints weight = 859.167| |-----------------------------------------------------------------------------| r_work (final): 0.3206 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061962 restraints weight = 539.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062408 restraints weight = 429.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062554 restraints weight = 375.335| |-----------------------------------------------------------------------------| r_work (final): 0.3294 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051374 restraints weight = 659.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051965 restraints weight = 429.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052407 restraints weight = 343.585| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 22 ARG 0.004 0.001 ARG M 16 *********************** REFINEMENT MACRO_CYCLE 7 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 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.022 Fit side-chains REVERT: I 19 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6181 (ptt90) REVERT: I 22 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7570 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.5252 time to fit residues: 1.6155 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 : 0.021 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 : 0.016 Fit side-chains REVERT: O 10 MET cc_start: 0.8115 (tpp) cc_final: 0.7803 (tmm) REVERT: O 23 ASP cc_start: 0.7489 (t0) cc_final: 0.7184 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0670 time to fit residues: 0.2998 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 : 0.015 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0348 time to fit residues: 0.1671 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 : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058375 restraints weight = 877.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058375 restraints weight = 885.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058375 restraints weight = 885.251| |-----------------------------------------------------------------------------| r_work (final): 0.3202 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062256 restraints weight = 464.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062526 restraints weight = 394.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062526 restraints weight = 356.959| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051315 restraints weight = 677.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052047 restraints weight = 437.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052435 restraints weight = 336.080| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR N 22 ARG 0.004 0.001 ARG B 16 *********************** 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 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Fit side-chains REVERT: I 19 ARG cc_start: 0.6990 (mtt180) cc_final: 0.6184 (ptt90) REVERT: I 22 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7571 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.5557 time to fit residues: 1.7066 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 : 0.015 Fit side-chains REVERT: O 10 MET cc_start: 0.8115 (tpp) cc_final: 0.7804 (tmm) REVERT: O 23 ASP cc_start: 0.7494 (t0) cc_final: 0.7186 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0653 time to fit residues: 0.2932 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 : 0.014 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0336 time to fit residues: 0.1608 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 : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058644 restraints weight = 803.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058624 restraints weight = 839.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058623 restraints weight = 841.536| |-----------------------------------------------------------------------------| r_work (final): 0.3211 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062045 restraints weight = 510.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.062445 restraints weight = 417.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062585 restraints weight = 370.149| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051287 restraints weight = 689.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051993 restraints weight = 443.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052195 restraints weight = 341.077| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR Q 22 ARG 0.004 0.001 ARG L 16 *********************** REFINEMENT MACRO_CYCLE 9 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 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Fit side-chains REVERT: I 19 ARG cc_start: 0.6982 (mtt180) cc_final: 0.6181 (ptt90) REVERT: I 22 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7569 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.5245 time to fit residues: 1.6106 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 : 0.019 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 : 0.015 Fit side-chains REVERT: O 10 MET cc_start: 0.8113 (tpp) cc_final: 0.7802 (tmm) REVERT: O 23 ASP cc_start: 0.7492 (t0) cc_final: 0.7185 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0646 time to fit residues: 0.2900 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 : 0.014 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0351 time to fit residues: 0.1679 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 : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 35 optimal weight: 0.0010 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.2080 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058513 restraints weight = 824.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058513 restraints weight = 860.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058513 restraints weight = 860.081| |-----------------------------------------------------------------------------| r_work (final): 0.3206 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062303 restraints weight = 450.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062638 restraints weight = 387.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062645 restraints weight = 353.602| |-----------------------------------------------------------------------------| r_work (final): 0.3296 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051236 restraints weight = 704.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051911 restraints weight = 448.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052400 restraints weight = 347.330| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR Q 22 ARG 0.004 0.001 ARG M 16 ********************** REFINEMENT MACRO_CYCLE 10 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 3 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.021 Fit side-chains REVERT: I 19 ARG cc_start: 0.6985 (mtt180) cc_final: 0.6188 (ptt90) REVERT: I 22 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7572 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.5388 time to fit residues: 1.6561 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 : 0.019 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 : 0.015 Fit side-chains REVERT: O 10 MET cc_start: 0.8123 (tpp) cc_final: 0.7808 (tmm) REVERT: O 23 ASP cc_start: 0.7493 (t0) cc_final: 0.7186 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0646 time to fit residues: 0.2909 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 : 0.014 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0353 time to fit residues: 0.1675 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 : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058620 restraints weight = 804.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058618 restraints weight = 839.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058618 restraints weight = 839.875| |-----------------------------------------------------------------------------| r_work (final): 0.3211 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062305 restraints weight = 463.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062501 restraints weight = 389.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062501 restraints weight = 359.122| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.051134 restraints weight = 741.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051878 restraints weight = 465.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052401 restraints weight = 351.560| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.8877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.162 Angle : 1.204 7.300 4176 Z= 0.508 Chirality : 0.092 0.221 438 Planarity : 0.009 0.066 522 Dihedral : 14.894 77.290 540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.48), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR O 22 ARG 0.004 0.001 ARG B 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.32 seconds wall clock time: 24 minutes 58.88 seconds (1498.88 seconds total)