Starting phenix.real_space_refine on Fri Aug 22 12:56:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967.map" model { file = "/net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yno_33967/08_2025/7yno_33967_neut.cif" } resolution = 2.8 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= 0.003 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 2 5.16 5 C 1618 2.51 5 N 442 2.21 5 O 500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2562 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D, E, F Time building chain proxies: 0.59, per 1000 atoms: 0.23 Number of scatterers: 2562 At special positions: 0 Unit cell: (100.43, 107.07, 32.37, 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 2 16.00 O 500 8.00 N 442 7.00 C 1618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 61.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 55 removed outlier: 5.770A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU F 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY A 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.719A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 6.351A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 5.867A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 45 through 55 removed outlier: 5.770A pdb=" N GLU C 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N VAL D 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY D 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA D 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL C 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N VAL D 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR E 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 61 through 63 removed outlier: 6.718A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 72 removed outlier: 6.351A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 78 removed outlier: 5.867A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA C 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 54 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 432 1.31 - 1.40: 512 1.40 - 1.49: 476 1.49 - 1.58: 1154 1.58 - 1.67: 4 Bond restraints: 2578 Sorted by residual: bond pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 1.766 1.670 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C07 IZV C 201 " pdb=" S16 IZV C 201 " ideal model delta sigma weight residual 1.766 1.670 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C11 IZV A 201 " pdb=" N12 IZV A 201 " ideal model delta sigma weight residual 1.351 1.442 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C11 IZV C 201 " pdb=" N12 IZV C 201 " ideal model delta sigma weight residual 1.351 1.442 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C07 IZV C 201 " pdb=" N06 IZV C 201 " ideal model delta sigma weight residual 1.290 1.373 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 2573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 3410 2.07 - 4.14: 62 4.14 - 6.21: 12 6.21 - 8.28: 2 8.28 - 10.36: 2 Bond angle restraints: 3488 Sorted by residual: angle pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " pdb=" C17 IZV A 201 " ideal model delta sigma weight residual 89.25 99.61 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C07 IZV C 201 " pdb=" S16 IZV C 201 " pdb=" C17 IZV C 201 " ideal model delta sigma weight residual 89.25 99.59 -10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C18 IZV A 201 " pdb=" C17 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 128.49 135.20 -6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" C18 IZV C 201 " pdb=" C17 IZV C 201 " pdb=" S16 IZV C 201 " ideal model delta sigma weight residual 128.49 135.18 -6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" N06 IZV A 201 " pdb=" C07 IZV A 201 " pdb=" S16 IZV A 201 " ideal model delta sigma weight residual 114.50 109.15 5.35 3.00e+00 1.11e-01 3.18e+00 ... (remaining 3483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.81: 1332 13.81 - 27.62: 120 27.62 - 41.43: 24 41.43 - 55.24: 0 55.24 - 69.04: 6 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA ALA F 90 " pdb=" C ALA F 90 " pdb=" N ALA F 91 " pdb=" CA ALA F 91 " ideal model delta harmonic sigma weight residual 180.00 165.63 14.37 0 5.00e+00 4.00e-02 8.26e+00 dihedral pdb=" CA ALA E 90 " pdb=" C ALA E 90 " pdb=" N ALA E 91 " pdb=" CA ALA E 91 " ideal model delta harmonic sigma weight residual 180.00 165.66 14.34 0 5.00e+00 4.00e-02 8.23e+00 dihedral pdb=" CA ALA B 90 " pdb=" C ALA B 90 " pdb=" N ALA B 91 " pdb=" CA ALA B 91 " ideal model delta harmonic sigma weight residual 180.00 165.67 14.33 0 5.00e+00 4.00e-02 8.22e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 194 0.026 - 0.052: 139 0.052 - 0.078: 45 0.078 - 0.104: 41 0.104 - 0.130: 37 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 453 not shown) Planarity restraints: 424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 IZV A 201 " -0.042 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" C08 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C09 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C10 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C11 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C14 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C15 IZV A 201 " 0.014 2.00e-02 2.50e+03 pdb=" N12 IZV A 201 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 IZV C 201 " 0.041 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" C08 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C09 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C10 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C11 IZV C 201 " -0.015 2.00e-02 2.50e+03 pdb=" C14 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" C15 IZV C 201 " -0.014 2.00e-02 2.50e+03 pdb=" N12 IZV C 201 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 38 " 0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C LEU C 38 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU C 38 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR C 39 " 0.005 2.00e-02 2.50e+03 ... (remaining 421 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 433 2.78 - 3.31: 2382 3.31 - 3.84: 3890 3.84 - 4.37: 4324 4.37 - 4.90: 8991 Nonbonded interactions: 20020 Sorted by model distance: nonbonded pdb=" ND2 ASN E 65 " pdb=" O GLY E 68 " model vdw 2.252 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.252 3.120 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.252 3.120 nonbonded pdb=" ND2 ASN F 65 " pdb=" O GLY F 68 " model vdw 2.252 3.120 nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.252 3.120 ... (remaining 20015 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.720 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.650 Find NCS groups from input model: 0.020 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 2578 Z= 0.382 Angle : 0.788 10.355 3488 Z= 0.409 Chirality : 0.054 0.130 456 Planarity : 0.003 0.024 424 Dihedral : 12.187 69.044 858 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -3.47 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 39 PHE 0.003 0.002 PHE B 94 HIS 0.006 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 2578) covalent geometry : angle 0.78847 ( 3488) hydrogen bonds : bond 0.23664 ( 18) hydrogen bonds : angle 10.61862 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2503 time to fit residues: 6.5852 Evaluate side-chains 17 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 79 GLN E 79 GLN F 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.222590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.183583 restraints weight = 2832.831| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 2.50 r_work: 0.4402 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2578 Z= 0.212 Angle : 0.586 3.786 3488 Z= 0.340 Chirality : 0.053 0.132 456 Planarity : 0.003 0.011 424 Dihedral : 5.712 14.888 366 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.33 % Allowed : 6.20 % Favored : 91.47 % 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: -2.70 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.004 0.002 PHE F 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 2578) covalent geometry : angle 0.58595 ( 3488) hydrogen bonds : bond 0.03772 ( 18) hydrogen bonds : angle 8.27412 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.062 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 29 average time/residue: 0.1387 time to fit residues: 4.3949 Evaluate side-chains 20 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.224578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.186645 restraints weight = 2880.849| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.48 r_work: 0.4428 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2578 Z= 0.153 Angle : 0.501 3.336 3488 Z= 0.294 Chirality : 0.052 0.129 456 Planarity : 0.002 0.010 424 Dihedral : 5.114 13.222 366 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.71 % Allowed : 5.81 % Favored : 91.47 % 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: -2.40 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.003 0.001 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2578) covalent geometry : angle 0.50102 ( 3488) hydrogen bonds : bond 0.03284 ( 18) hydrogen bonds : angle 7.90471 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.058 Fit side-chains REVERT: A 38 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5512 (tm) REVERT: B 38 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6496 (tm) REVERT: C 38 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5788 (tm) REVERT: E 38 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5824 (tm) REVERT: F 38 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5853 (tm) outliers start: 7 outliers final: 0 residues processed: 31 average time/residue: 0.2523 time to fit residues: 8.2558 Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4903 r_free = 0.4903 target = 0.221854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.183045 restraints weight = 2816.561| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 2.48 r_work: 0.4399 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2578 Z= 0.245 Angle : 0.606 4.550 3488 Z= 0.352 Chirality : 0.054 0.130 456 Planarity : 0.003 0.011 424 Dihedral : 5.622 14.663 366 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.71 % Allowed : 8.91 % Favored : 88.37 % 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: -2.23 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 39 PHE 0.005 0.002 PHE E 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 2578) covalent geometry : angle 0.60637 ( 3488) hydrogen bonds : bond 0.03915 ( 18) hydrogen bonds : angle 8.05411 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.098 Fit side-chains REVERT: F 38 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5949 (tp) outliers start: 7 outliers final: 0 residues processed: 29 average time/residue: 0.2196 time to fit residues: 6.8935 Evaluate side-chains 23 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.0060 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.226472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.189357 restraints weight = 2819.787| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 2.44 r_work: 0.4478 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2578 Z= 0.114 Angle : 0.473 4.734 3488 Z= 0.272 Chirality : 0.052 0.128 456 Planarity : 0.002 0.010 424 Dihedral : 4.747 12.156 366 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 10.85 % Favored : 86.82 % 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: -2.28 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.002 0.001 PHE C 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 2578) covalent geometry : angle 0.47297 ( 3488) hydrogen bonds : bond 0.02687 ( 18) hydrogen bonds : angle 7.59126 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.057 Fit side-chains REVERT: A 38 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5566 (tm) REVERT: B 38 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6534 (tm) outliers start: 6 outliers final: 1 residues processed: 28 average time/residue: 0.2113 time to fit residues: 6.3484 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.4898 r_free = 0.4898 target = 0.221645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.182937 restraints weight = 2859.353| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 2.48 r_work: 0.4401 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2578 Z= 0.256 Angle : 0.659 7.902 3488 Z= 0.364 Chirality : 0.055 0.181 456 Planarity : 0.003 0.011 424 Dihedral : 5.518 14.646 366 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.33 % Allowed : 15.50 % Favored : 82.17 % 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: -2.18 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.005 0.002 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 2578) covalent geometry : angle 0.65868 ( 3488) hydrogen bonds : bond 0.03906 ( 18) hydrogen bonds : angle 8.02235 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.103 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.2278 time to fit residues: 6.5590 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4949 r_free = 0.4949 target = 0.226603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.189500 restraints weight = 2802.690| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 2.43 r_work: 0.4479 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2578 Z= 0.109 Angle : 0.522 7.974 3488 Z= 0.279 Chirality : 0.053 0.159 456 Planarity : 0.002 0.010 424 Dihedral : 4.643 12.032 366 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.33 % Allowed : 15.89 % Favored : 81.78 % 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: -2.13 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.002 0.001 PHE F 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 2578) covalent geometry : angle 0.52178 ( 3488) hydrogen bonds : bond 0.02643 ( 18) hydrogen bonds : angle 7.60181 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.092 Fit side-chains REVERT: B 38 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6477 (tm) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.2036 time to fit residues: 6.5810 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4926 r_free = 0.4926 target = 0.224647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.186886 restraints weight = 2870.755| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 2.47 r_work: 0.4446 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2578 Z= 0.160 Angle : 0.601 10.689 3488 Z= 0.313 Chirality : 0.054 0.173 456 Planarity : 0.002 0.011 424 Dihedral : 4.827 13.155 366 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.71 % Allowed : 15.89 % Favored : 81.40 % 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: -2.05 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR F 39 PHE 0.003 0.001 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2578) covalent geometry : angle 0.60071 ( 3488) hydrogen bonds : bond 0.03111 ( 18) hydrogen bonds : angle 7.79446 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.057 Fit side-chains REVERT: B 38 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6449 (tm) outliers start: 7 outliers final: 3 residues processed: 30 average time/residue: 0.2149 time to fit residues: 6.8575 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.0000 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.4926 r_free = 0.4926 target = 0.224223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.186121 restraints weight = 2882.671| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 2.48 r_work: 0.4436 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2578 Z= 0.177 Angle : 0.620 9.400 3488 Z= 0.326 Chirality : 0.054 0.158 456 Planarity : 0.002 0.011 424 Dihedral : 4.948 13.549 366 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.40 % 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: -2.08 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 39 PHE 0.003 0.001 PHE F 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2578) covalent geometry : angle 0.62035 ( 3488) hydrogen bonds : bond 0.03296 ( 18) hydrogen bonds : angle 7.83984 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.098 Fit side-chains REVERT: B 38 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6486 (tm) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.2094 time to fit residues: 6.7380 Evaluate side-chains 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.221032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.183841 restraints weight = 2903.057| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 2.39 r_work: 0.4403 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2578 Z= 0.258 Angle : 0.692 7.743 3488 Z= 0.379 Chirality : 0.056 0.159 456 Planarity : 0.003 0.011 424 Dihedral : 5.571 14.713 366 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.33 % Allowed : 16.67 % Favored : 81.01 % 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: -2.18 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.005 0.002 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 2578) covalent geometry : angle 0.69171 ( 3488) hydrogen bonds : bond 0.03972 ( 18) hydrogen bonds : angle 8.05537 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.096 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 0.1577 time to fit residues: 4.9971 Evaluate side-chains 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4918 r_free = 0.4918 target = 0.224152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.187803 restraints weight = 2902.884| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 2.42 r_work: 0.4459 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4336 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2578 Z= 0.164 Angle : 0.612 8.136 3488 Z= 0.325 Chirality : 0.054 0.157 456 Planarity : 0.002 0.011 424 Dihedral : 5.061 13.552 366 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.94 % Allowed : 17.44 % Favored : 80.62 % 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: -2.14 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.003 0.001 PHE E 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2578) covalent geometry : angle 0.61168 ( 3488) hydrogen bonds : bond 0.03260 ( 18) hydrogen bonds : angle 7.87984 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 971.32 seconds wall clock time: 17 minutes 17.67 seconds (1037.67 seconds total)