Starting phenix.real_space_refine on Fri Aug 22 12:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppo_17806/08_2025/8ppo_17806.map" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 3 Type Number sf(0) Gaussians C 1088 2.51 5 N 272 2.21 5 O 336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1696 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "K" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "L" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "M" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 0.63, per 1000 atoms: 0.37 Number of scatterers: 1696 At special positions: 0 Unit cell: (69.1961, 40.2914, 55.1817, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 336 8.00 N 272 7.00 C 1088 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: 0.13 Conformation dependent library (CDL) restraints added in 65.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'I' and resid 306 through 310 Processing sheet with id=AA4, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.097A pdb=" N ASP L 314 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP N 314 " --> pdb=" O LEU O 315 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 hydrogen bond angles 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: 0.23 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 288 1.29 - 1.36: 240 1.36 - 1.42: 128 1.42 - 1.48: 272 1.48 - 1.54: 784 Bond restraints: 1712 Sorted by residual: bond pdb=" N GLY C 302 " pdb=" CA GLY C 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.65e+00 bond pdb=" N GLY G 302 " pdb=" CA GLY G 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.57e+00 bond pdb=" N GLY O 302 " pdb=" CA GLY O 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.47e+00 bond pdb=" N GLY K 302 " pdb=" CA GLY K 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.44e+00 bond pdb=" N GLY D 302 " pdb=" CA GLY D 302 " ideal model delta sigma weight residual 1.451 1.495 -0.044 1.60e-02 3.91e+03 7.41e+00 ... (remaining 1707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 2160 2.36 - 4.73: 136 4.73 - 7.09: 6 7.09 - 9.46: 0 9.46 - 11.82: 2 Bond angle restraints: 2304 Sorted by residual: angle pdb=" N TYR D 310 " pdb=" CA TYR D 310 " pdb=" C TYR D 310 " ideal model delta sigma weight residual 107.69 119.51 -11.82 2.01e+00 2.48e-01 3.46e+01 angle pdb=" N TYR L 310 " pdb=" CA TYR L 310 " pdb=" C TYR L 310 " ideal model delta sigma weight residual 108.02 118.24 -10.22 1.75e+00 3.27e-01 3.41e+01 angle pdb=" C TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta sigma weight residual 110.74 115.91 -5.17 1.61e+00 3.86e-01 1.03e+01 angle pdb=" CA TYR I 310 " pdb=" CB TYR I 310 " pdb=" CG TYR I 310 " ideal model delta sigma weight residual 113.90 118.69 -4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" CA TYR N 310 " pdb=" CB TYR N 310 " pdb=" CG TYR N 310 " ideal model delta sigma weight residual 113.90 118.59 -4.69 1.80e+00 3.09e-01 6.79e+00 ... (remaining 2299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.67: 871 10.67 - 21.33: 73 21.33 - 32.00: 16 32.00 - 42.66: 1 42.66 - 53.33: 31 Dihedral angle restraints: 992 sinusoidal: 368 harmonic: 624 Sorted by residual: dihedral pdb=" C TYR L 310 " pdb=" N TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta harmonic sigma weight residual -122.60 -134.88 12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C TYR D 310 " pdb=" N TYR D 310 " pdb=" CA TYR D 310 " pdb=" CB TYR D 310 " ideal model delta harmonic sigma weight residual -122.60 -133.55 10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" N TYR L 310 " pdb=" C TYR L 310 " pdb=" CA TYR L 310 " pdb=" CB TYR L 310 " ideal model delta harmonic sigma weight residual 122.80 131.75 -8.95 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 989 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.095: 230 0.095 - 0.190: 40 0.190 - 0.284: 0 0.284 - 0.378: 0 0.378 - 0.473: 2 Chirality restraints: 272 Sorted by residual: chirality pdb=" CA TYR L 310 " pdb=" N TYR L 310 " pdb=" C TYR L 310 " pdb=" CB TYR L 310 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA TYR D 310 " pdb=" N TYR D 310 " pdb=" C TYR D 310 " pdb=" CB TYR D 310 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA VAL H 309 " pdb=" N VAL H 309 " pdb=" C VAL H 309 " pdb=" CB VAL H 309 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 269 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 310 " -0.024 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR N 310 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR N 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR N 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR N 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR N 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR N 310 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR N 310 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.019 2.00e-02 2.50e+03 2.65e-02 1.40e+01 pdb=" CG TYR F 310 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.033 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.023 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR G 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.025 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 1084 3.08 - 3.54: 1371 3.54 - 3.99: 2495 3.99 - 4.45: 2858 4.45 - 4.90: 4710 Nonbonded interactions: 12518 Sorted by model distance: nonbonded pdb=" OH TYR A 310 " pdb=" O GLY I 303 " model vdw 2.625 3.040 nonbonded pdb=" OH TYR H 310 " pdb=" O GLY P 303 " model vdw 2.647 3.040 nonbonded pdb=" O GLY B 303 " pdb=" OH TYR I 310 " model vdw 2.683 3.040 nonbonded pdb=" O GLY C 303 " pdb=" OH TYR J 310 " model vdw 2.684 3.040 nonbonded pdb=" OH TYR E 310 " pdb=" O GLY M 303 " model vdw 2.694 3.040 ... (remaining 12513 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 individual isotropic 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: 8.980 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.008 0.044 1712 Z= 0.419 Angle : 1.197 11.822 2304 Z= 0.664 Chirality : 0.074 0.473 272 Planarity : 0.006 0.027 288 Dihedral : 13.412 53.329 608 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.55), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.55 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.046 0.012 TYR N 310 Details of bonding type rmsd covalent geometry : bond 0.00778 ( 1712) covalent geometry : angle 1.19732 ( 2304) hydrogen bonds : bond 0.15263 ( 71) hydrogen bonds : angle 9.19399 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.6586 time to fit residues: 21.4005 Evaluate side-chains 30 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.124418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.076665 restraints weight = 1434.196| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.43 r_work: 0.3278 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1712 Z= 0.140 Angle : 0.586 3.406 2304 Z= 0.308 Chirality : 0.057 0.136 272 Planarity : 0.004 0.019 288 Dihedral : 5.074 14.039 240 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.60), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.13 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR L 310 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1712) covalent geometry : angle 0.58557 ( 2304) hydrogen bonds : bond 0.05468 ( 71) hydrogen bonds : angle 6.24938 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6930 time to fit residues: 28.1132 Evaluate side-chains 37 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.075487 restraints weight = 1446.170| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.45 r_work: 0.3218 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.147 Angle : 0.551 3.354 2304 Z= 0.289 Chirality : 0.057 0.134 272 Planarity : 0.003 0.015 288 Dihedral : 5.092 13.708 240 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 5.73 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.14 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR L 310 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 1712) covalent geometry : angle 0.55083 ( 2304) hydrogen bonds : bond 0.05194 ( 71) hydrogen bonds : angle 5.87811 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.076 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.6695 time to fit residues: 25.1413 Evaluate side-chains 37 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain P residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.123352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.075863 restraints weight = 1403.615| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.42 r_work: 0.3219 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.153 Angle : 0.531 3.439 2304 Z= 0.277 Chirality : 0.057 0.134 272 Planarity : 0.003 0.014 288 Dihedral : 5.020 13.536 240 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 5.73 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.63), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.10 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 310 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 1712) covalent geometry : angle 0.53100 ( 2304) hydrogen bonds : bond 0.04918 ( 71) hydrogen bonds : angle 5.83084 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.055 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.7425 time to fit residues: 25.6244 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.124487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.077046 restraints weight = 1417.020| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.44 r_work: 0.3247 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1712 Z= 0.122 Angle : 0.503 3.396 2304 Z= 0.261 Chirality : 0.057 0.133 272 Planarity : 0.003 0.012 288 Dihedral : 4.872 13.495 240 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.04 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 310 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 1712) covalent geometry : angle 0.50326 ( 2304) hydrogen bonds : bond 0.04325 ( 71) hydrogen bonds : angle 5.68476 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.6789 time to fit residues: 23.4660 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.124044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.076525 restraints weight = 1427.638| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.45 r_work: 0.3230 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1712 Z= 0.130 Angle : 0.508 3.375 2304 Z= 0.263 Chirality : 0.057 0.133 272 Planarity : 0.002 0.012 288 Dihedral : 4.852 13.429 240 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 6.25 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.98 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 310 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 1712) covalent geometry : angle 0.50751 ( 2304) hydrogen bonds : bond 0.04419 ( 71) hydrogen bonds : angle 5.67806 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.062 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.6824 time to fit residues: 23.5601 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.076052 restraints weight = 1395.863| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.42 r_work: 0.3220 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.148 Angle : 0.517 3.349 2304 Z= 0.269 Chirality : 0.057 0.132 272 Planarity : 0.002 0.012 288 Dihedral : 4.879 13.474 240 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 5.73 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.94 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 310 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 1712) covalent geometry : angle 0.51724 ( 2304) hydrogen bonds : bond 0.04638 ( 71) hydrogen bonds : angle 5.75192 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.042 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.4239 time to fit residues: 14.6216 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain P residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.075768 restraints weight = 1418.724| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.45 r_work: 0.3212 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.161 Angle : 0.524 3.339 2304 Z= 0.272 Chirality : 0.057 0.132 272 Planarity : 0.002 0.012 288 Dihedral : 4.910 13.448 240 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 5.73 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.91 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 310 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 1712) covalent geometry : angle 0.52382 ( 2304) hydrogen bonds : bond 0.04747 ( 71) hydrogen bonds : angle 5.81124 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.041 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.4358 time to fit residues: 15.0781 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain P residue 305 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075753 restraints weight = 1408.329| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.44 r_work: 0.3220 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1712 Z= 0.161 Angle : 0.521 3.344 2304 Z= 0.271 Chirality : 0.057 0.133 272 Planarity : 0.002 0.012 288 Dihedral : 4.906 13.502 240 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.04 % Allowed : 6.25 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.89 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 310 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 1712) covalent geometry : angle 0.52085 ( 2304) hydrogen bonds : bond 0.04765 ( 71) hydrogen bonds : angle 5.82122 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.043 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.4639 time to fit residues: 16.0231 Evaluate side-chains 34 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain P residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075740 restraints weight = 1385.412| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.42 r_work: 0.3213 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.165 Angle : 0.524 3.370 2304 Z= 0.272 Chirality : 0.057 0.133 272 Planarity : 0.002 0.012 288 Dihedral : 4.928 13.526 240 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 6.77 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.64), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.88 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 310 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 1712) covalent geometry : angle 0.52424 ( 2304) hydrogen bonds : bond 0.04815 ( 71) hydrogen bonds : angle 5.83548 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 416 Ramachandran restraints generated. 208 Oldfield, 0 Emsley, 208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.042 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.5976 time to fit residues: 20.0002 Evaluate side-chains 33 residues out of total 192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 16 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.123044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.075396 restraints weight = 1425.651| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.46 r_work: 0.3205 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1712 Z= 0.172 Angle : 0.527 3.338 2304 Z= 0.274 Chirality : 0.057 0.132 272 Planarity : 0.002 0.012 288 Dihedral : 4.947 13.563 240 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.52 % Allowed : 6.77 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.65), residues: 208 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.89 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 310 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 1712) covalent geometry : angle 0.52723 ( 2304) hydrogen bonds : bond 0.04885 ( 71) hydrogen bonds : angle 5.85835 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.79 seconds wall clock time: 23 minutes 4.13 seconds (1384.13 seconds total)