Starting phenix.real_space_refine on Mon Feb 10 20:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol7_16953/02_2025/8ol7_16953.cif" } resolution = 3.0 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= 0.006 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1510 2.51 5 N 400 2.21 5 O 400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2320 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 232 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.61, per 1000 atoms: 0.69 Number of scatterers: 2320 At special positions: 0 Unit cell: (58.984, 71.912, 39.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 400 8.00 N 400 7.00 C 1510 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: 0.55 Conformation dependent library (CDL) restraints added in 305.3 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 10 through 13 removed outlier: 5.852A pdb=" N GLU J 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 16 through 18 removed outlier: 5.743A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 24 through 25 removed outlier: 6.613A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 30 through 36 removed outlier: 7.052A pdb=" N ILE J 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE H 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY J 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL H 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.613A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.651A pdb=" N LEU C 34 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 36 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL E 36 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 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: 0.56 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 750 1.34 - 1.45: 414 1.45 - 1.57: 1176 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2360 Sorted by residual: bond pdb=" C HIS B 13 " pdb=" O HIS B 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.54e-01 bond pdb=" C HIS D 13 " pdb=" O HIS D 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.40e-01 bond pdb=" C HIS J 13 " pdb=" O HIS J 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.39e-01 bond pdb=" C HIS C 13 " pdb=" O HIS C 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.32e-01 bond pdb=" CB PHE D 20 " pdb=" CG PHE D 20 " ideal model delta sigma weight residual 1.502 1.485 0.017 2.30e-02 1.89e+03 5.25e-01 ... (remaining 2355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2980 1.35 - 2.69: 120 2.69 - 4.04: 40 4.04 - 5.39: 10 5.39 - 6.74: 10 Bond angle restraints: 3160 Sorted by residual: angle pdb=" C VAL I 18 " pdb=" N PHE I 19 " pdb=" CA PHE I 19 " ideal model delta sigma weight residual 122.53 117.93 4.60 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C VAL G 18 " pdb=" N PHE G 19 " pdb=" CA PHE G 19 " ideal model delta sigma weight residual 122.53 117.94 4.59 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C VAL F 18 " pdb=" N PHE F 19 " pdb=" CA PHE F 19 " ideal model delta sigma weight residual 122.53 117.94 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C VAL B 18 " pdb=" N PHE B 19 " pdb=" CA PHE B 19 " ideal model delta sigma weight residual 122.53 117.96 4.57 1.92e+00 2.71e-01 5.68e+00 angle pdb=" C VAL D 18 " pdb=" N PHE D 19 " pdb=" CA PHE D 19 " ideal model delta sigma weight residual 122.53 117.96 4.57 1.92e+00 2.71e-01 5.66e+00 ... (remaining 3155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.50: 1020 8.50 - 16.99: 140 16.99 - 25.48: 50 25.48 - 33.97: 50 33.97 - 42.47: 20 Dihedral angle restraints: 1280 sinusoidal: 460 harmonic: 820 Sorted by residual: dihedral pdb=" CA LEU F 34 " pdb=" CB LEU F 34 " pdb=" CG LEU F 34 " pdb=" CD1 LEU F 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.89 42.11 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " pdb=" CG LEU H 34 " pdb=" CD1 LEU H 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.90 42.10 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" CA LEU J 34 " pdb=" CB LEU J 34 " pdb=" CG LEU J 34 " pdb=" CD1 LEU J 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 1277 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.031: 119 0.031 - 0.062: 131 0.062 - 0.093: 35 0.093 - 0.124: 50 0.124 - 0.154: 15 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA HIS H 14 " pdb=" N HIS H 14 " pdb=" C HIS H 14 " pdb=" CB HIS H 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA HIS D 14 " pdb=" N HIS D 14 " pdb=" C HIS D 14 " pdb=" CB HIS D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA HIS G 14 " pdb=" N HIS G 14 " pdb=" C HIS G 14 " pdb=" CB HIS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 347 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS I 13 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C HIS I 13 " 0.022 2.00e-02 2.50e+03 pdb=" O HIS I 13 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS I 14 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 13 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C HIS D 13 " -0.022 2.00e-02 2.50e+03 pdb=" O HIS D 13 " 0.008 2.00e-02 2.50e+03 pdb=" N HIS D 14 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 13 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C HIS H 13 " -0.022 2.00e-02 2.50e+03 pdb=" O HIS H 13 " 0.008 2.00e-02 2.50e+03 pdb=" N HIS H 14 " 0.007 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 1410 3.08 - 3.53: 2268 3.53 - 3.99: 3595 3.99 - 4.44: 4509 4.44 - 4.90: 8113 Nonbonded interactions: 19895 Sorted by model distance: nonbonded pdb=" OD1 ASP G 23 " pdb=" N ASP I 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP E 23 " pdb=" N ASP G 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP B 23 " pdb=" N ASP D 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP A 23 " pdb=" N ASP C 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP D 23 " pdb=" N ASP F 23 " model vdw 2.619 3.120 ... (remaining 19890 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.910 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.560 Find NCS groups from input model: 0.060 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.006 0.021 2360 Z= 0.386 Angle : 0.811 6.735 3160 Z= 0.430 Chirality : 0.066 0.154 350 Planarity : 0.003 0.013 400 Dihedral : 13.037 42.467 780 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.45), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 14 PHE 0.005 0.002 PHE I 19 TYR 0.006 0.002 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.255 Fit side-chains REVERT: E 28 LYS cc_start: 0.7623 (mttt) cc_final: 0.7393 (mttm) REVERT: F 28 LYS cc_start: 0.7349 (mttt) cc_final: 0.7134 (mttm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.9185 time to fit residues: 36.9129 Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.119942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.098996 restraints weight = 3045.149| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.72 r_work: 0.3971 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2360 Z= 0.232 Angle : 0.650 7.610 3160 Z= 0.346 Chirality : 0.060 0.139 350 Planarity : 0.002 0.006 400 Dihedral : 4.691 18.278 320 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.43 % Allowed : 10.00 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 14 PHE 0.007 0.002 PHE A 20 TYR 0.009 0.001 TYR E 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.257 Fit side-chains REVERT: B 28 LYS cc_start: 0.8014 (mttt) cc_final: 0.7742 (mttm) REVERT: E 28 LYS cc_start: 0.6950 (mttt) cc_final: 0.6672 (mttm) REVERT: F 28 LYS cc_start: 0.7321 (mttt) cc_final: 0.7011 (mttp) REVERT: I 26 SER cc_start: 0.7686 (m) cc_final: 0.7402 (t) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 1.4942 time to fit residues: 35.1852 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.095422 restraints weight = 3085.621| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.83 r_work: 0.3839 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2360 Z= 0.288 Angle : 0.640 7.897 3160 Z= 0.346 Chirality : 0.059 0.142 350 Planarity : 0.002 0.008 400 Dihedral : 4.808 18.462 320 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.87 % Allowed : 11.74 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS H 14 PHE 0.007 0.002 PHE I 19 TYR 0.007 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.245 Fit side-chains REVERT: A 28 LYS cc_start: 0.7924 (mttt) cc_final: 0.7664 (mttp) REVERT: B 28 LYS cc_start: 0.7959 (mttt) cc_final: 0.7633 (mttp) REVERT: E 28 LYS cc_start: 0.7014 (mttt) cc_final: 0.6731 (mttp) REVERT: F 28 LYS cc_start: 0.7246 (mttt) cc_final: 0.6906 (mttp) REVERT: I 26 SER cc_start: 0.7862 (m) cc_final: 0.7641 (t) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 1.5739 time to fit residues: 38.6204 Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.108883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.088405 restraints weight = 3172.799| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.70 r_work: 0.3740 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2360 Z= 0.459 Angle : 0.720 7.605 3160 Z= 0.399 Chirality : 0.063 0.146 350 Planarity : 0.003 0.008 400 Dihedral : 5.574 18.427 320 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.30 % Allowed : 11.74 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 13 PHE 0.009 0.003 PHE B 20 TYR 0.008 0.002 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.255 Fit side-chains REVERT: A 28 LYS cc_start: 0.7964 (mttt) cc_final: 0.7649 (mttp) REVERT: B 28 LYS cc_start: 0.7968 (mttt) cc_final: 0.7568 (mttm) REVERT: E 28 LYS cc_start: 0.7073 (mttt) cc_final: 0.6856 (mttp) REVERT: F 28 LYS cc_start: 0.7296 (mttt) cc_final: 0.7058 (mttp) REVERT: H 28 LYS cc_start: 0.7369 (ttmm) cc_final: 0.6754 (mttm) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 1.9224 time to fit residues: 45.0762 Evaluate side-chains 21 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.111722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.091054 restraints weight = 3194.476| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.74 r_work: 0.3740 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2360 Z= 0.388 Angle : 0.686 7.807 3160 Z= 0.377 Chirality : 0.062 0.143 350 Planarity : 0.002 0.008 400 Dihedral : 5.285 18.098 320 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 12.17 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 13 PHE 0.009 0.002 PHE J 19 TYR 0.007 0.002 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.227 Fit side-chains REVERT: J 15 GLN cc_start: 0.8915 (mp10) cc_final: 0.8697 (mp10) REVERT: A 15 GLN cc_start: 0.8839 (mp10) cc_final: 0.8567 (mp10) REVERT: A 28 LYS cc_start: 0.7897 (mttt) cc_final: 0.7666 (mttp) REVERT: B 28 LYS cc_start: 0.7848 (mttt) cc_final: 0.7557 (mttp) REVERT: E 28 LYS cc_start: 0.7058 (mttt) cc_final: 0.6765 (mttp) REVERT: F 28 LYS cc_start: 0.7209 (mttt) cc_final: 0.6861 (mttp) REVERT: H 28 LYS cc_start: 0.7312 (ttmm) cc_final: 0.6745 (mttm) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 1.8976 time to fit residues: 50.2230 Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.093459 restraints weight = 3133.082| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.75 r_work: 0.3783 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2360 Z= 0.287 Angle : 0.622 7.190 3160 Z= 0.342 Chirality : 0.060 0.140 350 Planarity : 0.002 0.007 400 Dihedral : 4.958 17.522 320 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.87 % Allowed : 12.61 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 13 PHE 0.007 0.002 PHE J 19 TYR 0.006 0.001 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.232 Fit side-chains REVERT: A 28 LYS cc_start: 0.7836 (mttt) cc_final: 0.7582 (mttp) REVERT: B 28 LYS cc_start: 0.7779 (mttt) cc_final: 0.7396 (mttp) REVERT: F 28 LYS cc_start: 0.7127 (mttt) cc_final: 0.6796 (mttp) REVERT: H 28 LYS cc_start: 0.7336 (ttmm) cc_final: 0.6813 (mttp) REVERT: I 28 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7042 (mttm) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 1.7661 time to fit residues: 46.7946 Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.114424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.093603 restraints weight = 3240.988| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.85 r_work: 0.3768 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2360 Z= 0.303 Angle : 0.638 6.950 3160 Z= 0.352 Chirality : 0.060 0.140 350 Planarity : 0.002 0.007 400 Dihedral : 5.016 16.916 320 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.87 % Allowed : 13.48 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 14 PHE 0.008 0.002 PHE J 19 TYR 0.006 0.001 TYR C 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.249 Fit side-chains REVERT: A 28 LYS cc_start: 0.7902 (mttt) cc_final: 0.7654 (mttp) REVERT: B 28 LYS cc_start: 0.7779 (mttt) cc_final: 0.7380 (mttp) REVERT: F 28 LYS cc_start: 0.7152 (mttt) cc_final: 0.6814 (mttp) REVERT: H 28 LYS cc_start: 0.7404 (ttmm) cc_final: 0.6889 (mttm) REVERT: I 28 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7092 (mttm) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 1.7242 time to fit residues: 40.4252 Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.110066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.090384 restraints weight = 3351.689| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.84 r_work: 0.3722 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2360 Z= 0.481 Angle : 0.735 6.711 3160 Z= 0.410 Chirality : 0.063 0.143 350 Planarity : 0.003 0.009 400 Dihedral : 5.550 15.291 320 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.87 % Allowed : 12.61 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 13 PHE 0.012 0.003 PHE B 20 TYR 0.008 0.002 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.250 Fit side-chains REVERT: A 28 LYS cc_start: 0.7944 (mttt) cc_final: 0.7674 (mttp) REVERT: B 28 LYS cc_start: 0.7842 (mttt) cc_final: 0.7455 (mttp) REVERT: H 28 LYS cc_start: 0.7424 (ttmm) cc_final: 0.7098 (mttp) REVERT: I 28 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7135 (mttm) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 1.8611 time to fit residues: 39.8605 Evaluate side-chains 22 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.118353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.099048 restraints weight = 2971.633| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.54 r_work: 0.3787 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2360 Z= 0.167 Angle : 0.550 6.781 3160 Z= 0.300 Chirality : 0.058 0.130 350 Planarity : 0.002 0.007 400 Dihedral : 4.649 19.342 320 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.87 % Allowed : 13.48 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 14 PHE 0.003 0.001 PHE F 19 TYR 0.008 0.001 TYR E 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.234 Fit side-chains REVERT: A 28 LYS cc_start: 0.7903 (mttt) cc_final: 0.7602 (mttp) REVERT: B 28 LYS cc_start: 0.7787 (mttt) cc_final: 0.7423 (mttm) REVERT: H 28 LYS cc_start: 0.7331 (ttmm) cc_final: 0.6801 (mttm) REVERT: I 28 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6964 (mttm) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 1.7299 time to fit residues: 38.8771 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.116819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.097837 restraints weight = 3062.968| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.57 r_work: 0.3749 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2360 Z= 0.233 Angle : 0.587 6.456 3160 Z= 0.323 Chirality : 0.058 0.135 350 Planarity : 0.002 0.007 400 Dihedral : 4.697 17.307 320 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.43 % Allowed : 13.91 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 14 PHE 0.006 0.002 PHE J 19 TYR 0.006 0.001 TYR E 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.251 Fit side-chains REVERT: A 28 LYS cc_start: 0.7914 (mttt) cc_final: 0.7612 (mttp) REVERT: B 28 LYS cc_start: 0.7798 (mttt) cc_final: 0.7360 (mttp) REVERT: H 28 LYS cc_start: 0.7365 (ttmm) cc_final: 0.6867 (mttm) REVERT: I 28 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7048 (mttp) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 1.7164 time to fit residues: 38.5891 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.110678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.090509 restraints weight = 3239.300| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.74 r_work: 0.3710 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2360 Z= 0.334 Angle : 0.647 6.538 3160 Z= 0.359 Chirality : 0.060 0.139 350 Planarity : 0.002 0.008 400 Dihedral : 5.016 16.136 320 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.43 % Allowed : 14.35 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 14 PHE 0.008 0.002 PHE B 20 TYR 0.007 0.002 TYR C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.64 seconds wall clock time: 33 minutes 54.66 seconds (2034.66 seconds total)