Starting phenix.real_space_refine on Fri May 9 15:47:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb1_61304/05_2025/9jb1_61304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb1_61304/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jb1_61304/05_2025/9jb1_61304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb1_61304/05_2025/9jb1_61304.map" model { file = "/net/cci-nas-00/data/ceres_data/9jb1_61304/05_2025/9jb1_61304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb1_61304/05_2025/9jb1_61304.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3012 Number of models: 1 Model: "" Number of chains: 2 Chain: "FP" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "FP" 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: FQ, FF, FG, FH, FI, FJ, FK, FL, FM, FN, FO Time building chain proxies: 1.70, per 1000 atoms: 0.56 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: 0.83 Conformation dependent library (CDL) restraints added in 347.1 milliseconds 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: 0.59 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: 0.95 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: 0.03 Found NCS groups: ncs_group { reference = chain 'FP' selection = chain 'FQ' selection = chain 'FF' selection = chain 'FG' selection = chain 'FH' selection = chain 'FI' selection = chain 'FJ' selection = chain 'FK' selection = chain 'FL' selection = chain 'FM' selection = chain 'FN' selection = chain 'FO' } 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: 1.940 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (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 HIS 0.003 0.001 HISFK 13 PHE 0.004 0.001 PHEFN 20 TYR 0.002 0.000 TYRFN 10 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 12) link_TRANS : angle 0.10865 ( 36) covalent geometry : bond 0.00143 ( 3048) covalent geometry : angle 0.60012 ( 4080) *********************** 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 : 0.363 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 1.0567 time to fit residues: 83.6498 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 : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.113082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087340 restraints weight = 3196.075| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.21 r_work: 0.3180 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3060 Z= 0.220 Angle : 0.536 6.168 4116 Z= 0.280 Chirality : 0.058 0.123 468 Planarity : 0.002 0.006 516 Dihedral : 4.630 14.183 432 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.39 % Allowed : 17.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.41), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISFN 13 PHE 0.013 0.003 PHEFQ 20 TYR 0.008 0.002 TYRFH 10 Details of bonding type rmsd link_TRANS : bond 0.00078 ( 12) link_TRANS : angle 0.24372 ( 36) covalent geometry : bond 0.00499 ( 3048) covalent geometry : angle 0.53779 ( 4080) *********************** 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 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.351 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 1.2031 time to fit residues: 72.9038 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 : 0.338 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.112749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.087490 restraints weight = 3155.253| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.16 r_work: 0.3183 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3060 Z= 0.193 Angle : 0.514 6.597 4116 Z= 0.268 Chirality : 0.058 0.122 468 Planarity : 0.002 0.006 516 Dihedral : 4.942 23.040 432 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 17.01 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISFN 13 PHE 0.011 0.003 PHEFQ 20 TYR 0.007 0.001 TYRFH 10 Details of bonding type rmsd link_TRANS : bond 0.00063 ( 12) link_TRANS : angle 0.22265 ( 36) covalent geometry : bond 0.00432 ( 3048) covalent geometry : angle 0.51622 ( 4080) *********************** 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 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.350 Fit side-chains REVERT: FM 11 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7569 (mt-10) REVERT: FH 35 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.7345 (tpt) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 1.2498 time to fit residues: 73.1532 Evaluate side-chains 58 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.118538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093666 restraints weight = 3180.061| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.15 r_work: 0.3275 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3060 Z= 0.132 Angle : 0.477 6.824 4116 Z= 0.243 Chirality : 0.057 0.120 468 Planarity : 0.001 0.005 516 Dihedral : 4.637 23.616 432 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.04 % Allowed : 17.01 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISFH 13 PHE 0.009 0.002 PHEFQ 20 TYR 0.005 0.001 TYRFK 10 Details of bonding type rmsd link_TRANS : bond 0.00036 ( 12) link_TRANS : angle 0.18681 ( 36) covalent geometry : bond 0.00290 ( 3048) covalent geometry : angle 0.47914 ( 4080) *********************** 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 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.352 Fit side-chains REVERT: FP 35 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8146 (tpt) REVERT: FL 28 LYS cc_start: 0.8914 (mttm) cc_final: 0.8705 (mttp) REVERT: FH 35 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.7378 (tpt) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 1.2027 time to fit residues: 72.9792 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 : 0.342 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.110536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085171 restraints weight = 3258.222| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.18 r_work: 0.3148 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3060 Z= 0.271 Angle : 0.572 6.678 4116 Z= 0.303 Chirality : 0.059 0.120 468 Planarity : 0.002 0.007 516 Dihedral : 5.679 31.771 432 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.08 % Allowed : 14.24 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.39), 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 HIS 0.004 0.002 HISFN 13 PHE 0.014 0.003 PHEFQ 20 TYR 0.008 0.002 TYRFP 10 Details of bonding type rmsd link_TRANS : bond 0.00088 ( 12) link_TRANS : angle 0.28481 ( 36) covalent geometry : bond 0.00616 ( 3048) covalent geometry : angle 0.57392 ( 4080) *********************** 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 61 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.347 Fit side-chains REVERT: FP 35 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.7897 (tpt) REVERT: FM 11 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7730 (mt-10) REVERT: FH 35 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.7367 (tpt) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 1.2673 time to fit residues: 72.8393 Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FO residue 26 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.089472 restraints weight = 3260.779| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.20 r_work: 0.3230 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3060 Z= 0.187 Angle : 0.530 6.965 4116 Z= 0.272 Chirality : 0.058 0.122 468 Planarity : 0.002 0.006 516 Dihedral : 5.440 31.788 432 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.08 % Allowed : 14.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISFN 13 PHE 0.011 0.003 PHEFQ 20 TYR 0.007 0.001 TYRFP 10 Details of bonding type rmsd link_TRANS : bond 0.00058 ( 12) link_TRANS : angle 0.26621 ( 36) covalent geometry : bond 0.00421 ( 3048) covalent geometry : angle 0.53154 ( 4080) *********************** 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: 6 poor density : 55 time to evaluate : 0.338 Fit side-chains REVERT: FO 35 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8541 (tpt) REVERT: FP 35 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8144 (tpt) REVERT: FM 11 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7709 (mt-10) REVERT: FH 35 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.7381 (tpt) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 1.1163 time to fit residues: 64.3106 Evaluate side-chains 56 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.112544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087376 restraints weight = 3211.126| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.19 r_work: 0.3203 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3060 Z= 0.265 Angle : 0.586 7.982 4116 Z= 0.306 Chirality : 0.059 0.121 468 Planarity : 0.002 0.007 516 Dihedral : 5.968 34.543 432 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.78 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.39), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HISFN 13 PHE 0.014 0.003 PHEFQ 20 TYR 0.008 0.002 TYRFP 10 Details of bonding type rmsd link_TRANS : bond 0.00090 ( 12) link_TRANS : angle 0.30436 ( 36) covalent geometry : bond 0.00605 ( 3048) covalent geometry : angle 0.58765 ( 4080) *********************** 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 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.343 Fit side-chains REVERT: FO 35 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8620 (tpt) REVERT: FP 35 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8156 (tpt) REVERT: FM 11 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7802 (mt-10) REVERT: FJ 35 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8534 (tpt) REVERT: FH 35 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.7387 (tpt) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 1.2157 time to fit residues: 71.1544 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 FJ residue 35 MET Chi-restraints excluded: chain FI residue 26 SER Chi-restraints excluded: chain FH residue 35 MET Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.115795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.091048 restraints weight = 3210.718| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.16 r_work: 0.3258 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3060 Z= 0.145 Angle : 0.524 8.431 4116 Z= 0.260 Chirality : 0.058 0.122 468 Planarity : 0.001 0.005 516 Dihedral : 5.280 29.381 432 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.08 % Allowed : 13.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (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 HIS 0.004 0.001 HISFH 13 PHE 0.010 0.002 PHEFQ 20 TYR 0.006 0.001 TYRFP 10 Details of bonding type rmsd link_TRANS : bond 0.00051 ( 12) link_TRANS : angle 0.22458 ( 36) covalent geometry : bond 0.00324 ( 3048) covalent geometry : angle 0.52549 ( 4080) *********************** 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: 6 poor density : 55 time to evaluate : 0.315 Fit side-chains REVERT: FP 35 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8179 (tpt) REVERT: FM 11 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7677 (mt-10) REVERT: FH 35 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.7397 (tpt) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 1.2579 time to fit residues: 72.3216 Evaluate side-chains 58 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain FF residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.113351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.088212 restraints weight = 3242.577| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.20 r_work: 0.3222 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3060 Z= 0.225 Angle : 0.576 8.406 4116 Z= 0.293 Chirality : 0.058 0.122 468 Planarity : 0.002 0.007 516 Dihedral : 5.648 29.769 432 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.08 % Allowed : 12.85 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISFN 13 PHE 0.012 0.003 PHEFQ 20 TYR 0.008 0.002 TYRFK 10 Details of bonding type rmsd link_TRANS : bond 0.00063 ( 12) link_TRANS : angle 0.27390 ( 36) covalent geometry : bond 0.00513 ( 3048) covalent geometry : angle 0.57804 ( 4080) *********************** 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 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.326 Fit side-chains REVERT: FO 35 MET cc_start: 0.9226 (tpt) cc_final: 0.8830 (tpt) REVERT: FP 35 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8228 (tpt) REVERT: FM 11 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7718 (mt-10) REVERT: FH 35 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.7396 (tpt) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 1.2359 time to fit residues: 68.5779 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FO residue 26 SER 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 23 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.114652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089964 restraints weight = 3161.463| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.15 r_work: 0.3241 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3060 Z= 0.187 Angle : 0.560 8.918 4116 Z= 0.279 Chirality : 0.058 0.121 468 Planarity : 0.002 0.006 516 Dihedral : 5.519 28.394 432 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HISFP 13 PHE 0.012 0.002 PHEFQ 20 TYR 0.007 0.001 TYRFK 10 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 12) link_TRANS : angle 0.23856 ( 36) covalent geometry : bond 0.00424 ( 3048) covalent geometry : angle 0.56174 ( 4080) ********************** 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 60 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.354 Fit side-chains REVERT: FO 35 MET cc_start: 0.9228 (tpt) cc_final: 0.8781 (tpt) REVERT: FP 35 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8184 (tpt) REVERT: FM 11 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7704 (mt-10) REVERT: FH 35 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.7400 (tpt) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 1.1434 time to fit residues: 64.6956 Evaluate side-chains 59 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain FO residue 26 SER 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 33 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 22 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.116680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092067 restraints weight = 3163.006| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.14 r_work: 0.3272 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3060 Z= 0.137 Angle : 0.535 8.919 4116 Z= 0.260 Chirality : 0.058 0.121 468 Planarity : 0.001 0.005 516 Dihedral : 5.131 25.094 432 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.74 % Allowed : 13.19 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.40), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISFH 13 PHE 0.009 0.002 PHEFQ 20 TYR 0.006 0.001 TYRFP 10 Details of bonding type rmsd link_TRANS : bond 0.00039 ( 12) link_TRANS : angle 0.20483 ( 36) covalent geometry : bond 0.00307 ( 3048) covalent geometry : angle 0.53696 ( 4080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.79 seconds wall clock time: 46 minutes 2.27 seconds (2762.27 seconds total)