Starting phenix.real_space_refine on Wed Mar 5 14:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.cif Found real_map, /net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.map" model { file = "/net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6og3_20051/03_2025/6og3_20051.cif" } resolution = 4.1 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 2 Type Number sf(0) Gaussians C 810 2.51 5 N 405 2.21 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1215 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 396 Classifications: {'peptide': 132} Incomplete info: {'n_c_alpha_c_only': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 135 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 210 Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 27 Classifications: {'peptide': 9} Incomplete info: {'n_c_alpha_c_only': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.02, per 1000 atoms: 1.66 Number of scatterers: 1215 At special positions: 0 Unit cell: (54.696, 80.496, 75.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 2 Type Number sf(0) N 405 7.00 C 810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 381.6 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'E' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 7 through 24' Processing helix chain 'E' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 30 through 40' Processing helix chain 'E' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 45 through 54' Processing helix chain 'E' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 56 through 69' Processing helix chain 'E' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 84 through 102' Processing helix chain 'E' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 107 through 117' Processing helix chain 'E' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 119 through 129' Processing helix chain 'E' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'E' and resid 132 through 142' Processing helix chain 'C' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 7 through 24' Processing helix chain 'C' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 30 through 40' Processing helix chain 'C' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 45 through 54' Processing helix chain 'C' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 56 through 69' Processing helix chain 'C' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 84 through 102' Processing helix chain 'C' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 107 through 117' Processing helix chain 'C' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 119 through 129' Processing helix chain 'C' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'C' and resid 132 through 142' Processing helix chain 'A' and resid 7 through 24 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 7 through 24' Processing helix chain 'A' and resid 30 through 40 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 30 through 40' Processing helix chain 'A' and resid 45 through 54 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 45 through 54' Processing helix chain 'A' and resid 56 through 69 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 56 through 69' Processing helix chain 'A' and resid 84 through 102 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 84 through 102' Processing helix chain 'A' and resid 107 through 117 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 107 through 117' Processing helix chain 'A' and resid 119 through 129 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 119 through 129' Processing helix chain 'A' and resid 132 through 142 WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! WARNING: missing atoms! No H-bonds generated for 'chain 'A' and resid 132 through 142' 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: 0.07 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.32 - 1.37: 398 1.37 - 1.41: 0 1.41 - 1.45: 19 1.45 - 1.49: 386 1.49 - 1.54: 405 Bond restraints: 1208 Sorted by residual: bond pdb=" N ASP E 4 " pdb=" CA ASP E 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 bond pdb=" N ASP C 4 " pdb=" CA ASP C 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.40e+00 bond pdb=" N ASP A 4 " pdb=" CA ASP A 4 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.29e+00 bond pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 1.516 1.536 -0.020 1.72e-02 3.38e+03 1.33e+00 bond pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 1.456 1.471 -0.015 1.33e-02 5.65e+03 1.29e+00 ... (remaining 1203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 881 1.41 - 2.82: 245 2.82 - 4.22: 51 4.22 - 5.63: 15 5.63 - 7.04: 9 Bond angle restraints: 1201 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 110.42 117.09 -6.67 9.60e-01 1.09e+00 4.83e+01 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 110.42 117.08 -6.66 9.60e-01 1.09e+00 4.82e+01 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 110.42 117.07 -6.65 9.60e-01 1.09e+00 4.81e+01 angle pdb=" N THR E 121 " pdb=" CA THR E 121 " pdb=" C THR E 121 " ideal model delta sigma weight residual 111.07 116.67 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" N THR A 121 " pdb=" CA THR A 121 " pdb=" C THR A 121 " ideal model delta sigma weight residual 111.07 116.61 -5.54 1.07e+00 8.73e-01 2.68e+01 ... (remaining 1196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 0.84: 275 0.84 - 1.69: 96 1.69 - 2.53: 20 2.53 - 3.37: 3 3.37 - 4.22: 4 Dihedral angle restraints: 398 sinusoidal: 0 harmonic: 398 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 175.78 4.22 0 5.00e+00 4.00e-02 7.11e-01 dihedral pdb=" CA PHE E 28 " pdb=" C PHE E 28 " pdb=" N ILE E 29 " pdb=" CA ILE E 29 " ideal model delta harmonic sigma weight residual 180.00 176.36 3.64 0 5.00e+00 4.00e-02 5.31e-01 dihedral pdb=" CA PHE C 28 " pdb=" C PHE C 28 " pdb=" N ILE C 29 " pdb=" CA ILE C 29 " ideal model delta harmonic sigma weight residual 180.00 176.47 3.53 0 5.00e+00 4.00e-02 4.97e-01 ... (remaining 395 not shown) Chirality restraints: 0 Planarity restraints: 0 Histogram of nonbonded interaction distances: 2.54 - 3.01: 471 3.01 - 3.48: 547 3.48 - 3.95: 768 3.95 - 4.43: 1587 4.43 - 4.90: 2121 Nonbonded interactions: 5494 Sorted by model distance: nonbonded pdb=" N ARG E 5 " pdb=" N LEU E 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG A 5 " pdb=" N LEU A 6 " model vdw 2.539 2.560 nonbonded pdb=" N ARG C 5 " pdb=" N LEU C 6 " model vdw 2.541 2.560 nonbonded pdb=" N ALA C 53 " pdb=" N GLY C 54 " model vdw 2.629 2.560 nonbonded pdb=" N ALA E 53 " pdb=" N GLY E 54 " model vdw 2.630 2.560 ... (remaining 5489 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.000 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: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4858 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 : 0.005 0.031 1208 Z= 0.393 Angle : 1.530 7.041 1201 Z= 1.235 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 0.934 4.216 398 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 0.00 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.27 (0.36), residues: 384 helix: 0.09 (0.24), residues: 318 sheet: None (None), residues: 0 loop : 1.54 (0.68), residues: 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.177 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0321 time to fit residues: 0.3821 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.0270 chunk 19 optimal weight: 0.2980 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 0.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049027 restraints weight = 11724.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049027 restraints weight = 11893.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049027 restraints weight = 11894.313| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.000 0.002 1208 Z= 0.020 Angle : 0.107 0.428 1201 Z= 0.081 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 1.583 3.560 398 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 3.84 (0.43), residues: 384 helix: 2.61 (0.29), residues: 318 sheet: None (None), residues: 0 loop : 2.38 (0.74), residues: 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.177 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0134 time to fit residues: 0.3513 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 overall best weight: 9.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.034490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2226 r_free = 0.2226 target = 0.024482 restraints weight = 13310.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.024578 restraints weight = 12491.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.024578 restraints weight = 11910.633| |-----------------------------------------------------------------------------| r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 1.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.024 1208 Z= 0.523 Angle : 1.058 5.515 1201 Z= 0.797 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.870 23.705 398 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 41.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.60 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.31 (0.39), residues: 384 helix: -1.30 (0.33), residues: 177 sheet: None (None), residues: 0 loop : 1.09 (0.41), residues: 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.167 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0134 time to fit residues: 0.3387 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.0270 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 10 optimal weight: 0.0170 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 0.0000 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 4.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.034059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.024118 restraints weight = 13254.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2211 r_free = 0.2211 target = 0.024164 restraints weight = 12614.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2214 r_free = 0.2214 target = 0.024228 restraints weight = 12245.709| |-----------------------------------------------------------------------------| r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 1.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 1208 Z= 0.238 Angle : 0.570 3.317 1201 Z= 0.446 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.285 16.900 398 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.04 (0.41), residues: 384 helix: -0.47 (0.35), residues: 201 sheet: None (None), residues: 0 loop : 0.91 (0.44), residues: 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.175 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0132 time to fit residues: 0.3430 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 0.0370 chunk 1 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 overall best weight: 7.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.033307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.024807 restraints weight = 12266.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2269 r_free = 0.2269 target = 0.024645 restraints weight = 14278.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.024609 restraints weight = 14458.737| |-----------------------------------------------------------------------------| r_work (final): 0.2244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 1.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 1208 Z= 0.419 Angle : 0.848 3.759 1201 Z= 0.662 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 8.110 20.964 398 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 42.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.07 (0.41), residues: 384 helix: -1.52 (0.37), residues: 169 sheet: None (None), residues: 0 loop : 0.17 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.174 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0132 time to fit residues: 0.3476 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 0.0060 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 7 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 overall best weight: 3.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.033327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2293 r_free = 0.2293 target = 0.024766 restraints weight = 12230.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.024697 restraints weight = 12738.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2287 r_free = 0.2287 target = 0.024741 restraints weight = 13323.974| |-----------------------------------------------------------------------------| r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 1.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.009 1208 Z= 0.196 Angle : 0.501 2.659 1201 Z= 0.403 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.176 17.543 398 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.56 (0.42), residues: 384 helix: -0.82 (0.38), residues: 183 sheet: None (None), residues: 0 loop : 0.29 (0.42), residues: 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.171 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0129 time to fit residues: 0.3466 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 overall best weight: 7.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.032628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.024383 restraints weight = 12543.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2261 r_free = 0.2261 target = 0.024317 restraints weight = 12970.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2263 r_free = 0.2263 target = 0.024364 restraints weight = 13641.006| |-----------------------------------------------------------------------------| r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 1.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 1208 Z= 0.392 Angle : 0.802 3.857 1201 Z= 0.631 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.985 21.156 398 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 42.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.71 (0.41), residues: 384 helix: -1.87 (0.36), residues: 181 sheet: None (None), residues: 0 loop : -0.24 (0.42), residues: 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.171 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0128 time to fit residues: 0.3383 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 0.0000 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.0050 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.032015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2187 r_free = 0.2187 target = 0.023331 restraints weight = 14246.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.023479 restraints weight = 13026.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.023481 restraints weight = 12056.796| |-----------------------------------------------------------------------------| r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 1.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.008 1208 Z= 0.207 Angle : 0.528 2.831 1201 Z= 0.424 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 6.554 17.933 398 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.08 (0.42), residues: 384 helix: -1.18 (0.39), residues: 183 sheet: None (None), residues: 0 loop : -0.07 (0.43), residues: 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.153 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0106 time to fit residues: 0.2742 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 0.0470 chunk 29 optimal weight: 20.0000 overall best weight: 7.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.031369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.022655 restraints weight = 14172.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.022789 restraints weight = 12744.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2157 r_free = 0.2157 target = 0.022908 restraints weight = 11774.936| |-----------------------------------------------------------------------------| r_work (final): 0.2198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 1.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 1208 Z= 0.371 Angle : 0.771 3.921 1201 Z= 0.609 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.667 19.957 398 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 43.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.50 (0.42), residues: 384 helix: -1.75 (0.40), residues: 162 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.177 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0136 time to fit residues: 0.3524 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.032151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2252 r_free = 0.2252 target = 0.023915 restraints weight = 12776.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.023877 restraints weight = 13018.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.023922 restraints weight = 13622.209| |-----------------------------------------------------------------------------| r_work (final): 0.2226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 1.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 1208 Z= 0.343 Angle : 0.735 3.820 1201 Z= 0.582 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.567 19.992 398 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 42.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.21 (0.41), residues: 384 helix: -1.52 (0.44), residues: 142 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.159 Fit side-chains TARDY: cannot create tardy model for: "MET E 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 35 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A 35 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0229 time to fit residues: 0.4198 Evaluate side-chains 3 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 7 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 7.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.031782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.023673 restraints weight = 13065.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2231 r_free = 0.2231 target = 0.023597 restraints weight = 12781.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.023628 restraints weight = 13762.023| |-----------------------------------------------------------------------------| r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 1.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 1208 Z= 0.380 Angle : 0.795 4.023 1201 Z= 0.628 Chirality : 0.000 0.000 0 Planarity : 0.000 0.000 0 Dihedral : 7.924 21.085 398 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 46.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.43 (0.41), residues: 384 helix: -1.69 (0.45), residues: 135 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 708.87 seconds wall clock time: 13 minutes 11.31 seconds (791.31 seconds total)