Starting phenix.real_space_refine on Wed Mar 5 15:58:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yno_33967/03_2025/7yno_33967_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yno_33967/03_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_33967/03_2025/7yno_33967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yno_33967/03_2025/7yno_33967.map" model { file = "/net/cci-nas-00/data/ceres_data/7yno_33967/03_2025/7yno_33967_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yno_33967/03_2025/7yno_33967_neut.cif" } resolution = 2.8 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= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: E, D, F, C Time building chain proxies: 2.27, per 1000 atoms: 0.89 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: 0.73 Conformation dependent library (CDL) restraints added in 372.3 milliseconds 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: 0.31 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: 0.51 Time building geometry restraints manager: 0.82 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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= 0.441 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 : 22.12 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 (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: -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 HIS 0.006 0.004 HIS D 50 PHE 0.003 0.002 PHE B 94 TYR 0.006 0.002 TYR B 39 *********************** 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 : 0.259 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.7372 time to fit residues: 19.3653 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 : 0.262 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN C 79 GLN D 79 GLN E 79 GLN F 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.225865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.188447 restraints weight = 2817.818| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.46 r_work: 0.4439 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2578 Z= 0.192 Angle : 0.505 3.343 3488 Z= 0.290 Chirality : 0.052 0.129 456 Planarity : 0.002 0.010 424 Dihedral : 5.127 12.890 366 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.71 % Allowed : 5.04 % Favored : 92.25 % 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: -2.68 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.002 0.001 PHE C 94 TYR 0.004 0.001 TYR A 39 *********************** 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 36 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.275 Fit side-chains REVERT: C 38 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5890 (tm) REVERT: E 38 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5718 (tm) outliers start: 7 outliers final: 0 residues processed: 36 average time/residue: 0.8533 time to fit residues: 31.8939 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4976 r_free = 0.4976 target = 0.229997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.194649 restraints weight = 2798.439| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 2.37 r_work: 0.4513 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2578 Z= 0.121 Angle : 0.441 6.020 3488 Z= 0.248 Chirality : 0.052 0.123 456 Planarity : 0.002 0.011 424 Dihedral : 4.456 10.620 366 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 8.53 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (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 HIS 0.004 0.002 HIS E 50 PHE 0.002 0.001 PHE B 94 TYR 0.004 0.001 TYR F 39 *********************** 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 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.273 Fit side-chains REVERT: A 38 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5431 (tm) REVERT: B 38 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6513 (tm) REVERT: E 38 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5770 (tm) outliers start: 6 outliers final: 0 residues processed: 29 average time/residue: 0.8779 time to fit residues: 26.4887 Evaluate side-chains 21 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 = 0.4923 r_free = 0.4923 target = 0.224936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.187089 restraints weight = 2843.360| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.49 r_work: 0.4432 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2578 Z= 0.249 Angle : 0.528 6.930 3488 Z= 0.298 Chirality : 0.053 0.130 456 Planarity : 0.002 0.011 424 Dihedral : 4.840 13.416 366 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.49 % Allowed : 10.08 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.003 0.002 PHE E 94 TYR 0.006 0.002 TYR E 39 *********************** 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 34 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.258 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 33 average time/residue: 0.5990 time to fit residues: 20.8670 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.2590 ------------------------------------------------------------------------------- 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 = 0.4948 r_free = 0.4948 target = 0.227245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.190008 restraints weight = 2829.223| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.47 r_work: 0.4477 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2578 Z= 0.177 Angle : 0.496 7.067 3488 Z= 0.273 Chirality : 0.052 0.128 456 Planarity : 0.002 0.010 424 Dihedral : 4.510 12.033 366 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.33 % Allowed : 11.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.002 0.001 PHE E 94 TYR 0.005 0.001 TYR A 39 *********************** 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 29 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.276 Fit side-chains REVERT: A 38 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5336 (tm) REVERT: B 38 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6447 (tm) REVERT: D 38 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6369 (tm) outliers start: 6 outliers final: 1 residues processed: 29 average time/residue: 0.5150 time to fit residues: 15.9914 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 D residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4928 r_free = 0.4928 target = 0.225060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.187134 restraints weight = 2852.995| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 2.47 r_work: 0.4441 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2578 Z= 0.240 Angle : 0.536 6.555 3488 Z= 0.301 Chirality : 0.053 0.128 456 Planarity : 0.002 0.010 424 Dihedral : 4.809 13.358 366 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.10 % Allowed : 10.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (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 HIS 0.004 0.003 HIS A 50 PHE 0.003 0.002 PHE E 94 TYR 0.006 0.002 TYR E 39 *********************** 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 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.263 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 31 average time/residue: 0.5499 time to fit residues: 18.1063 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.4912 r_free = 0.4912 target = 0.223219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.184733 restraints weight = 2875.765| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.49 r_work: 0.4412 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2578 Z= 0.298 Angle : 0.593 6.586 3488 Z= 0.331 Chirality : 0.054 0.130 456 Planarity : 0.002 0.010 424 Dihedral : 5.094 13.948 366 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.55 % Allowed : 12.40 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.004 0.002 PHE E 94 TYR 0.007 0.002 TYR A 39 *********************** 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 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.284 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.3505 time to fit residues: 10.8158 Evaluate side-chains 25 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 0.0370 chunk 15 optimal weight: 6.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- 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 = 0.4951 r_free = 0.4951 target = 0.227192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.190435 restraints weight = 2818.705| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.41 r_work: 0.4486 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2129 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= 0.157 Angle : 0.507 7.332 3488 Z= 0.275 Chirality : 0.052 0.130 456 Planarity : 0.002 0.010 424 Dihedral : 4.478 11.722 366 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.55 % Allowed : 13.57 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.002 0.001 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** 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 27 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.281 Fit side-chains REVERT: E 38 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5942 (tm) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.3691 time to fit residues: 10.9238 Evaluate side-chains 24 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4890 ------------------------------------------------------------------------------- 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 = 0.4983 r_free = 0.4983 target = 0.230607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.195012 restraints weight = 2840.531| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 2.40 r_work: 0.4546 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2578 Z= 0.101 Angle : 0.518 12.396 3488 Z= 0.256 Chirality : 0.053 0.192 456 Planarity : 0.002 0.013 424 Dihedral : 3.963 9.606 366 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.94 % Allowed : 13.57 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.001 0.000 PHE B 94 TYR 0.004 0.001 TYR F 39 *********************** 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 28 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.256 Fit side-chains REVERT: B 38 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6383 (tm) REVERT: B 43 LYS cc_start: 0.8354 (mttt) cc_final: 0.6304 (pttp) REVERT: D 38 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6490 (tm) REVERT: D 43 LYS cc_start: 0.8384 (mttt) cc_final: 0.6452 (pttp) outliers start: 5 outliers final: 1 residues processed: 28 average time/residue: 0.8373 time to fit residues: 24.4451 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 : 0.279 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.4895 r_free = 0.4895 target = 0.221345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.182505 restraints weight = 2853.207| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 2.48 r_work: 0.4384 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2578 Z= 0.418 Angle : 0.774 13.435 3488 Z= 0.401 Chirality : 0.057 0.198 456 Planarity : 0.003 0.014 424 Dihedral : 5.322 14.429 366 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.94 % Allowed : 14.34 % Favored : 83.72 % 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: -2.04 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.007 0.003 PHE B 94 TYR 0.008 0.002 TYR B 39 ********************** 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 31 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.432 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 0.4886 time to fit residues: 15.6767 Evaluate side-chains 26 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 = 0.4929 r_free = 0.4929 target = 0.225313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.188265 restraints weight = 2887.498| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.44 r_work: 0.4451 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2204 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= 0.268 Angle : 0.696 12.636 3488 Z= 0.347 Chirality : 0.055 0.183 456 Planarity : 0.002 0.012 424 Dihedral : 4.974 13.837 366 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.78 % Allowed : 15.89 % 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: -2.07 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.003 0.002 PHE E 94 TYR 0.006 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.04 seconds wall clock time: 34 minutes 38.43 seconds (2078.43 seconds total)