Starting phenix.real_space_refine on Wed Sep 17 03:20:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb1_61304/09_2025/9jb1_61304.map" } resolution = 2.5 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1956 2.51 5 N 504 2.21 5 O 540 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3012 Number of models: 1 Model: "" Number of chains: 2 Chain: "FO" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "FO" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Restraints were copied for chains: FP, FN, FM, FL, FQ, FK, FJ, FI, FH, FG, FF Time building chain proxies: 0.50, per 1000 atoms: 0.17 Number of scatterers: 3012 At special positions: 0 Unit cell: (70.55, 68.89, 44.82, 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 12 16.00 O 540 8.00 N 504 7.00 C 1956 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 Links applied TRANS " DASFF 23 " - " GLUFF 22 " " DASFG 23 " - " GLUFG 22 " " DASFH 23 " - " GLUFH 22 " " DASFI 23 " - " GLUFI 22 " " DASFJ 23 " - " GLUFJ 22 " " DASFK 23 " - " GLUFK 22 " " DASFL 23 " - " GLUFL 22 " " DASFM 23 " - " GLUFM 22 " " DASFN 23 " - " GLUFN 22 " " DASFO 23 " - " GLUFO 22 " " DASFP 23 " - " GLUFP 22 " " DASFQ 23 " - " GLUFQ 22 " Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 139.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DASFO 23 " pdb=" CB DASFP 23 " pdb=" CB DASFN 23 " pdb=" CB DASFM 23 " pdb=" CB DASFL 23 " pdb=" CB DASFQ 23 " pdb=" CB DASFK 23 " pdb=" CB DASFJ 23 " pdb=" CB DASFI 23 " pdb=" CB DASFH 23 " pdb=" CB DASFG 23 " pdb=" CB DASFF 23 " Number of C-beta restraints generated: 648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.45: 391 1.45 - 1.57: 1661 1.57 - 1.68: 0 1.68 - 1.79: 24 Bond restraints: 3048 Sorted by residual: bond pdb=" CB LEUFP 34 " pdb=" CG LEUFP 34 " ideal model delta sigma weight residual 1.530 1.538 -0.008 2.00e-02 2.50e+03 1.72e-01 bond pdb=" CB LEUFG 34 " pdb=" CG LEUFG 34 " ideal model delta sigma weight residual 1.530 1.538 -0.008 2.00e-02 2.50e+03 1.71e-01 bond pdb=" CB LEUFM 34 " pdb=" CG LEUFM 34 " ideal model delta sigma weight residual 1.530 1.538 -0.008 2.00e-02 2.50e+03 1.71e-01 bond pdb=" CG METFJ 35 " pdb=" SD METFJ 35 " ideal model delta sigma weight residual 1.803 1.793 0.010 2.50e-02 1.60e+03 1.71e-01 bond pdb=" CB LEUFN 34 " pdb=" CG LEUFN 34 " ideal model delta sigma weight residual 1.530 1.538 -0.008 2.00e-02 2.50e+03 1.62e-01 ... (remaining 3043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 4004 1.48 - 2.95: 40 2.95 - 4.43: 24 4.43 - 5.90: 0 5.90 - 7.38: 12 Bond angle restraints: 4080 Sorted by residual: angle pdb=" CA LEUFN 34 " pdb=" CB LEUFN 34 " pdb=" CG LEUFN 34 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.45e+00 angle pdb=" CA LEUFO 34 " pdb=" CB LEUFO 34 " pdb=" CG LEUFO 34 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.45e+00 angle pdb=" CA LEUFH 34 " pdb=" CB LEUFH 34 " pdb=" CG LEUFH 34 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.44e+00 angle pdb=" CA LEUFL 34 " pdb=" CB LEUFL 34 " pdb=" CG LEUFL 34 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.44e+00 angle pdb=" CA LEUFI 34 " pdb=" CB LEUFI 34 " pdb=" CG LEUFI 34 " ideal model delta sigma weight residual 116.30 123.68 -7.38 3.50e+00 8.16e-02 4.44e+00 ... (remaining 4075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.41: 1368 12.41 - 24.83: 156 24.83 - 37.24: 72 37.24 - 49.65: 60 49.65 - 62.06: 48 Dihedral angle restraints: 1704 sinusoidal: 648 harmonic: 1056 Sorted by residual: dihedral pdb=" CB METFI 35 " pdb=" CG METFI 35 " pdb=" SD METFI 35 " pdb=" CE METFI 35 " ideal model delta sinusoidal sigma weight residual -180.00 -124.05 -55.95 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB METFQ 35 " pdb=" CG METFQ 35 " pdb=" SD METFQ 35 " pdb=" CE METFQ 35 " ideal model delta sinusoidal sigma weight residual -180.00 -124.06 -55.94 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB METFO 35 " pdb=" CG METFO 35 " pdb=" SD METFO 35 " pdb=" CE METFO 35 " ideal model delta sinusoidal sigma weight residual -180.00 -124.07 -55.93 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 192 0.024 - 0.048: 95 0.048 - 0.072: 85 0.072 - 0.096: 0 0.096 - 0.120: 96 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILEFK 31 " pdb=" N ILEFK 31 " pdb=" C ILEFK 31 " pdb=" CB ILEFK 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILEFI 31 " pdb=" N ILEFI 31 " pdb=" C ILEFI 31 " pdb=" CB ILEFI 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILEFH 31 " pdb=" N ILEFH 31 " pdb=" C ILEFH 31 " pdb=" CB ILEFH 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 465 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HISFJ 13 " 0.002 2.00e-02 2.50e+03 4.44e-03 1.97e-01 pdb=" C HISFJ 13 " -0.008 2.00e-02 2.50e+03 pdb=" O HISFJ 13 " 0.003 2.00e-02 2.50e+03 pdb=" N HISFJ 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HISFG 13 " 0.002 2.00e-02 2.50e+03 4.43e-03 1.96e-01 pdb=" C HISFG 13 " -0.008 2.00e-02 2.50e+03 pdb=" O HISFG 13 " 0.003 2.00e-02 2.50e+03 pdb=" N HISFG 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HISFL 13 " -0.002 2.00e-02 2.50e+03 4.38e-03 1.92e-01 pdb=" C HISFL 13 " 0.008 2.00e-02 2.50e+03 pdb=" O HISFL 13 " -0.003 2.00e-02 2.50e+03 pdb=" N HISFL 14 " -0.003 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 2127 3.11 - 3.56: 3051 3.56 - 4.00: 5283 4.00 - 4.45: 5498 4.45 - 4.90: 10685 Nonbonded interactions: 26644 Sorted by model distance: nonbonded pdb=" N LYSFG 28 " pdb=" O ASNFF 27 " model vdw 2.660 3.120 nonbonded pdb=" N LYSFJ 28 " pdb=" O ASNFI 27 " model vdw 2.663 3.120 nonbonded pdb=" N PHEFJ 20 " pdb=" O PHEFI 19 " model vdw 2.671 3.120 nonbonded pdb=" N LYSFN 28 " pdb=" O ASNFM 27 " model vdw 2.676 3.120 nonbonded pdb=" O ASNFO 27 " pdb=" N LYSFP 28 " model vdw 2.683 3.120 ... (remaining 26639 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: 0.01 Found NCS groups: ncs_group { reference = chain 'FO' selection = chain 'FP' selection = chain 'FN' selection = chain 'FM' selection = chain 'FL' selection = chain 'FQ' selection = chain 'FK' selection = chain 'FJ' selection = chain 'FI' selection = chain 'FH' selection = chain 'FG' selection = chain 'FF' } 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.001 0.010 3060 Z= 0.081 Angle : 0.598 7.380 4116 Z= 0.264 Chirality : 0.058 0.120 468 Planarity : 0.001 0.004 516 Dihedral : 19.338 62.060 1020 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 29.17 % Favored : 70.83 % 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: -0.86 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYRFN 10 PHE 0.004 0.001 PHEFN 20 HIS 0.003 0.001 HISFK 13 Details of bonding type rmsd covalent geometry : bond 0.00143 ( 3048) covalent geometry : angle 0.60012 ( 4080) link_TRANS : bond 0.00042 ( 12) link_TRANS : angle 0.10865 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.5216 time to fit residues: 41.2125 Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087961 restraints weight = 3249.203| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.17 r_work: 0.3191 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3060 Z= 0.190 Angle : 0.517 6.118 4116 Z= 0.269 Chirality : 0.057 0.124 468 Planarity : 0.002 0.005 516 Dihedral : 4.451 12.486 432 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.39 % Allowed : 17.71 % Favored : 80.90 % 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: -0.89 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRFH 10 PHE 0.012 0.003 PHEFQ 20 HIS 0.004 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 3048) covalent geometry : angle 0.51840 ( 4080) link_TRANS : bond 0.00077 ( 12) link_TRANS : angle 0.20922 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.131 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.6436 time to fit residues: 39.5923 Evaluate side-chains 58 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FI residue 26 SER Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.109194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083611 restraints weight = 3301.436| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.21 r_work: 0.3107 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.062 3060 Z= 0.435 Angle : 0.681 5.893 4116 Z= 0.373 Chirality : 0.062 0.120 468 Planarity : 0.003 0.009 516 Dihedral : 6.584 38.882 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.08 % Allowed : 15.28 % Favored : 82.64 % 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: -1.54 (0.38), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYRFP 10 PHE 0.020 0.005 PHEFQ 20 HIS 0.005 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00993 ( 3048) covalent geometry : angle 0.68380 ( 4080) link_TRANS : bond 0.00158 ( 12) link_TRANS : angle 0.31703 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.204 Fit side-chains REVERT: FH 35 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.7321 (tpt) REVERT: FG 11 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7862 (tt0) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 0.6712 time to fit residues: 42.6540 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FI residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.119183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094764 restraints weight = 3188.385| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.16 r_work: 0.3306 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3060 Z= 0.089 Angle : 0.462 6.994 4116 Z= 0.233 Chirality : 0.058 0.126 468 Planarity : 0.001 0.005 516 Dihedral : 5.012 31.087 432 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 1.39 % Allowed : 15.28 % Favored : 83.33 % 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: -1.31 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYRFP 10 PHE 0.007 0.001 PHEFQ 20 HIS 0.003 0.001 HISFH 13 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 3048) covalent geometry : angle 0.46340 ( 4080) link_TRANS : bond 0.00025 ( 12) link_TRANS : angle 0.19987 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.111 Fit side-chains REVERT: FO 35 MET cc_start: 0.9207 (tpt) cc_final: 0.8693 (tpt) REVERT: FP 35 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8160 (tpt) REVERT: FL 28 LYS cc_start: 0.8880 (mttm) cc_final: 0.8671 (mttp) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.5496 time to fit residues: 36.1735 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.116601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091682 restraints weight = 3170.479| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.19 r_work: 0.3268 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3060 Z= 0.141 Angle : 0.500 6.786 4116 Z= 0.251 Chirality : 0.057 0.121 468 Planarity : 0.001 0.005 516 Dihedral : 5.003 29.114 432 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 14.24 % Favored : 84.38 % 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: -1.25 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYRFM 10 PHE 0.010 0.002 PHEFQ 20 HIS 0.004 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3048) covalent geometry : angle 0.50172 ( 4080) link_TRANS : bond 0.00036 ( 12) link_TRANS : angle 0.19483 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.125 Fit side-chains REVERT: FP 35 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8115 (tpt) REVERT: FH 35 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.7672 (tpt) outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.5687 time to fit residues: 34.4458 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.112855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087785 restraints weight = 3276.269| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.19 r_work: 0.3203 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3060 Z= 0.282 Angle : 0.589 6.400 4116 Z= 0.312 Chirality : 0.059 0.120 468 Planarity : 0.002 0.007 516 Dihedral : 5.911 33.790 432 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.43 % Allowed : 12.85 % Favored : 84.72 % 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: -1.40 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRFM 10 PHE 0.015 0.003 PHEFQ 20 HIS 0.005 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 3048) covalent geometry : angle 0.59087 ( 4080) link_TRANS : bond 0.00097 ( 12) link_TRANS : angle 0.27598 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.124 Fit side-chains REVERT: FO 35 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8678 (tpt) REVERT: FP 35 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8187 (tpt) REVERT: FM 11 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7815 (mt-10) REVERT: FH 35 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.7543 (tpt) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.5992 time to fit residues: 33.7690 Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FO residue 26 SER Chi-restraints excluded: chain FO residue 35 MET Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.118418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094046 restraints weight = 3215.842| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.15 r_work: 0.3293 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3060 Z= 0.105 Angle : 0.495 7.566 4116 Z= 0.244 Chirality : 0.058 0.124 468 Planarity : 0.001 0.005 516 Dihedral : 4.957 27.479 432 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.04 % Allowed : 14.58 % Favored : 84.38 % 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: -1.25 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYRFM 10 PHE 0.008 0.002 PHEFQ 20 HIS 0.003 0.001 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3048) covalent geometry : angle 0.49696 ( 4080) link_TRANS : bond 0.00029 ( 12) link_TRANS : angle 0.17628 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.073 Fit side-chains REVERT: FP 35 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8280 (tpt) REVERT: FJ 22 GLU cc_start: 0.7633 (tt0) cc_final: 0.7354 (tt0) REVERT: FH 35 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.7560 (tpt) outliers start: 3 outliers final: 0 residues processed: 59 average time/residue: 0.5578 time to fit residues: 33.7864 Evaluate side-chains 58 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FH residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.114369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089178 restraints weight = 3155.284| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.20 r_work: 0.3255 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3060 Z= 0.156 Angle : 0.527 7.362 4116 Z= 0.263 Chirality : 0.058 0.121 468 Planarity : 0.002 0.006 516 Dihedral : 5.090 26.581 432 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.39 % Allowed : 14.24 % Favored : 84.38 % 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: -1.25 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYRFM 10 PHE 0.010 0.002 PHEFQ 20 HIS 0.004 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3048) covalent geometry : angle 0.52923 ( 4080) link_TRANS : bond 0.00040 ( 12) link_TRANS : angle 0.20259 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.071 Fit side-chains REVERT: FO 35 MET cc_start: 0.9219 (tpt) cc_final: 0.8743 (tpt) REVERT: FP 35 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8187 (tpt) REVERT: FM 11 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7689 (mt-10) REVERT: FJ 22 GLU cc_start: 0.7680 (tt0) cc_final: 0.7384 (tt0) REVERT: FH 35 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.7587 (tpt) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.5846 time to fit residues: 34.6398 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 11 GLU Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.116319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091508 restraints weight = 3271.997| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.19 r_work: 0.3268 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3060 Z= 0.152 Angle : 0.531 7.570 4116 Z= 0.263 Chirality : 0.058 0.121 468 Planarity : 0.002 0.005 516 Dihedral : 5.062 25.289 432 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.74 % Allowed : 14.24 % Favored : 84.03 % 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: -1.26 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYRFM 10 PHE 0.010 0.002 PHEFQ 20 HIS 0.003 0.002 HISFP 13 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3048) covalent geometry : angle 0.53283 ( 4080) link_TRANS : bond 0.00037 ( 12) link_TRANS : angle 0.19867 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.125 Fit side-chains REVERT: FO 35 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8572 (tpt) REVERT: FP 35 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8225 (tpt) REVERT: FJ 22 GLU cc_start: 0.7636 (tt0) cc_final: 0.7336 (tt0) REVERT: FH 35 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.7573 (tpt) outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 0.5847 time to fit residues: 34.7970 Evaluate side-chains 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FO residue 35 MET Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 11 GLU Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 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 = 0.3737 r_free = 0.3737 target = 0.114105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.089186 restraints weight = 3134.593| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.17 r_work: 0.3258 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3060 Z= 0.160 Angle : 0.539 7.607 4116 Z= 0.268 Chirality : 0.058 0.121 468 Planarity : 0.002 0.005 516 Dihedral : 5.109 24.865 432 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.08 % Allowed : 13.54 % Favored : 84.38 % 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 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRFM 10 PHE 0.011 0.002 PHEFQ 20 HIS 0.004 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3048) covalent geometry : angle 0.54152 ( 4080) link_TRANS : bond 0.00039 ( 12) link_TRANS : angle 0.20039 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.122 Fit side-chains REVERT: FP 35 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8189 (tpt) REVERT: FM 11 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7668 (mt-10) REVERT: FJ 22 GLU cc_start: 0.7666 (tt0) cc_final: 0.7363 (tt0) REVERT: FH 35 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.7572 (tpt) outliers start: 6 outliers final: 3 residues processed: 58 average time/residue: 0.5964 time to fit residues: 35.4358 Evaluate side-chains 62 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FP residue 35 MET Chi-restraints excluded: chain FL residue 11 GLU Chi-restraints excluded: chain FL residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.115988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091317 restraints weight = 3205.593| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.17 r_work: 0.3268 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3060 Z= 0.155 Angle : 0.533 7.651 4116 Z= 0.265 Chirality : 0.058 0.121 468 Planarity : 0.002 0.005 516 Dihedral : 5.087 24.178 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.74 % Allowed : 13.89 % Favored : 84.38 % 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: -1.26 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRFM 10 PHE 0.010 0.002 PHEFQ 20 HIS 0.004 0.002 HISFN 13 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3048) covalent geometry : angle 0.53469 ( 4080) link_TRANS : bond 0.00038 ( 12) link_TRANS : angle 0.19725 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.73 seconds wall clock time: 25 minutes 9.34 seconds (1509.34 seconds total)