Starting phenix.real_space_refine on Fri May 9 22:13:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9u_45371/05_2025/9c9u_45371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9u_45371/05_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_45371/05_2025/9c9u_45371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9u_45371/05_2025/9c9u_45371.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9u_45371/05_2025/9c9u_45371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9u_45371/05_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-5687/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: 1.48, per 1000 atoms: 0.49 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: 0.82 Conformation dependent library (CDL) restraints added in 179.1 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: 0.60 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.93 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.730 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd covalent geometry : bond 0.01128 ( 3114) covalent geometry : angle 1.48255 ( 4176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.4769 time to fit residues: 3.3880 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 : 0.015 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: 0.0941 time to fit residues: 0.4094 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: 0.0608 time to fit residues: 0.3964 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=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 = 0.061634 restraints weight = 892.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061613 restraints weight = 930.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061613 restraints weight = 914.022| |-----------------------------------------------------------------------------| 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 = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062345 restraints weight = 579.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062356 restraints weight = 469.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062368 restraints weight = 468.107| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-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 = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057122 restraints weight = 717.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057836 restraints weight = 455.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058204 restraints weight = 349.856| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 B 22 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 3114) covalent geometry : angle 1.32016 ( 4176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 330 Ramachandran restraints generated. 165 Oldfield, 0 Emsley, 165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 330 Ramachandran restraints generated. 165 Oldfield, 0 Emsley, 165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 13 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.023 Fit side-chains REVERT: I 19 ARG cc_start: 0.6900 (mtt180) cc_final: 0.6337 (ptm-80) REVERT: I 22 ARG cc_start: 0.8271 (mmp80) cc_final: 0.7588 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.3865 time to fit residues: 2.3665 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: 0.8313 (t0) cc_final: 0.8041 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0705 time to fit residues: 0.3164 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: 0.0345 time to fit residues: 0.1634 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 : 0.011 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 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 = 0.3636 r_free = 0.3636 target = 0.077245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058969 restraints weight = 814.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059397 restraints weight = 659.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059519 restraints weight = 584.455| |-----------------------------------------------------------------------------| r_work (final): 0.3198 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.082986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061310 restraints weight = 663.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061326 restraints weight = 640.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061326 restraints weight = 635.641| |-----------------------------------------------------------------------------| r_work (final): 0.3184 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.061727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050192 restraints weight = 829.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050713 restraints weight = 574.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050999 restraints weight = 463.616| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.8429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.027 3114 Z= 0.371 Angle : 1.288 8.418 4176 Z= 0.550 Chirality : 0.103 0.274 438 Planarity : 0.011 0.066 522 Dihedral : 15.793 80.747 540 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.63 (0.42), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.32), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR N 22 ARG 0.005 0.002 ARG M 22 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 3114) covalent geometry : angle 1.28800 ( 4176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 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: J 19 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6238 (ptm-80) REVERT: J 22 ARG cc_start: 0.8189 (mmp80) cc_final: 0.7264 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.5624 time to fit residues: 2.2922 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: 0.7336 (t0) cc_final: 0.7053 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0661 time to fit residues: 0.2956 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0357 time to fit residues: 0.1709 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.075150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058470 restraints weight = 872.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058448 restraints weight = 891.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058448 restraints weight = 903.173| |-----------------------------------------------------------------------------| r_work (final): 0.3193 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.084646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061400 restraints weight = 594.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061400 restraints weight = 587.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061400 restraints weight = 587.091| |-----------------------------------------------------------------------------| r_work (final): 0.3151 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050852 restraints weight = 776.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051339 restraints weight = 561.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051867 restraints weight = 474.585| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.8892 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 : 1.209 8.198 4176 Z= 0.512 Chirality : 0.097 0.244 438 Planarity : 0.011 0.078 522 Dihedral : 15.498 81.608 540 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 18.37 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: -3.46 (0.47), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.36), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR O 22 ARG 0.004 0.001 ARG L 22 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 3114) covalent geometry : angle 1.20897 ( 4176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 274 Ramachandran restraints generated. 137 Oldfield, 0 Emsley, 137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 274 Ramachandran restraints generated. 137 Oldfield, 0 Emsley, 137 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: I 19 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6279 (ptt90) REVERT: I 22 ARG cc_start: 0.8210 (mmp80) cc_final: 0.7658 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.4983 time to fit residues: 2.0309 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 : 0.019 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 : 0.014 Fit side-chains REVERT: N 23 ASP cc_start: 0.7473 (t0) cc_final: 0.7166 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0605 time to fit residues: 0.2706 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: 0.0324 time to fit residues: 0.1201 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 ------------------------------------------------------------------------------- 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: 0.5980 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.0060 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.066682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052901 restraints weight = 1020.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.053225 restraints weight = 828.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053365 restraints weight = 742.676| |-----------------------------------------------------------------------------| r_work (final): 0.3096 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062463 restraints weight = 538.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.063173 restraints weight = 385.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.063173 restraints weight = 315.342| |-----------------------------------------------------------------------------| r_work (final): 0.3316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048488 restraints weight = 873.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049034 restraints weight = 655.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049054 restraints weight = 557.162| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.8897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3114 Z= 0.273 Angle : 1.195 8.098 4176 Z= 0.506 Chirality : 0.093 0.221 438 Planarity : 0.010 0.073 522 Dihedral : 15.545 81.728 540 Min Nonbonded Distance : 2.549 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: -3.49 (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 0.007 0.002 TYR N 22 ARG 0.004 0.001 ARG B 22 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 3114) covalent geometry : angle 1.19513 ( 4176) *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.022 Fit side-chains REVERT: L 19 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6482 (ptt90) REVERT: L 22 ARG cc_start: 0.8118 (mmp80) cc_final: 0.7626 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.5273 time to fit residues: 2.1514 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: O 10 MET cc_start: 0.8139 (tpp) cc_final: 0.7701 (tmm) REVERT: O 23 ASP cc_start: 0.7580 (t0) cc_final: 0.7259 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0658 time to fit residues: 0.2952 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.1311 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: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 31 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.066937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052351 restraints weight = 881.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052351 restraints weight = 726.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052351 restraints weight = 726.675| |-----------------------------------------------------------------------------| r_work (final): 0.3063 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062426 restraints weight = 555.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062922 restraints weight = 393.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.063466 restraints weight = 329.817| |-----------------------------------------------------------------------------| r_work (final): 0.3319 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050688 restraints weight = 754.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051366 restraints weight = 548.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051821 restraints weight = 444.697| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.8904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3114 Z= 0.273 Angle : 1.195 8.098 4176 Z= 0.506 Chirality : 0.093 0.221 438 Planarity : 0.010 0.073 522 Dihedral : 15.545 81.728 540 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 18.37 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: -3.49 (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 0.007 0.002 TYR R 22 ARG 0.004 0.001 ARG B 22 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 3114) covalent geometry : angle 1.19513 ( 4176) *********************** 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 : 0.020 Fit side-chains REVERT: L 19 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6474 (ptt90) REVERT: L 22 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7627 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.5181 time to fit residues: 2.1133 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 : 0.019 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 : 0.014 Fit side-chains REVERT: O 10 MET cc_start: 0.8144 (tpp) cc_final: 0.7700 (tmm) REVERT: O 23 ASP cc_start: 0.7581 (t0) cc_final: 0.7260 (t0) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0637 time to fit residues: 0.2870 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 : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0348 time to fit residues: 0.1302 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3092 > 50: distance: 0 - 1: 12.684 distance: 1 - 2: 40.291 distance: 1 - 4: 28.827 distance: 2 - 3: 22.136 distance: 2 - 8: 57.540 distance: 4 - 5: 28.022 distance: 4 - 6: 20.832 distance: 5 - 7: 3.317 distance: 8 - 9: 21.585 distance: 8 - 14: 46.110 distance: 9 - 12: 41.722 distance: 10 - 11: 21.339 distance: 10 - 16: 20.594 distance: 12 - 13: 41.130 distance: 13 - 14: 10.457 distance: 13 - 15: 19.927 distance: 16 - 17: 35.317 distance: 18 - 19: 40.278 distance: 20 - 21: 39.685 distance: 21 - 22: 40.644 distance: 21 - 24: 40.174 distance: 22 - 23: 7.694 distance: 22 - 27: 40.881 distance: 24 - 25: 68.593 distance: 27 - 28: 39.839 distance: 27 - 33: 55.579 distance: 28 - 29: 39.149 distance: 28 - 31: 57.440 distance: 31 - 32: 39.436 distance: 32 - 33: 56.566 distance: 35 - 36: 41.471 distance: 36 - 37: 48.578 distance: 37 - 39: 40.787 distance: 39 - 40: 40.883 distance: 39 - 45: 40.494 distance: 40 - 41: 44.763 distance: 40 - 43: 11.392 distance: 41 - 42: 11.364 distance: 41 - 46: 49.291 distance: 43 - 44: 39.967 distance: 44 - 45: 39.643 distance: 47 - 48: 56.434 distance: 48 - 54: 56.186 distance: 50 - 51: 55.827 distance: 51 - 53: 40.424 distance: 54 - 55: 39.741 distance: 55 - 56: 40.810 distance: 56 - 58: 68.657 distance: 59 - 60: 14.918 distance: 60 - 61: 41.397 distance: 63 - 64: 40.049 distance: 64 - 65: 4.482