Starting phenix.real_space_refine on Mon Feb 10 19:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbp_61322/02_2025/9jbp_61322_neut.cif" } resolution = 3.18 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: 3 Type Number sf(0) Gaussians C 1278 2.51 5 N 354 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 297 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: I, H, K, J, L, C, B, E, D, F Time building chain proxies: 2.44, per 1000 atoms: 1.21 Number of scatterers: 2022 At special positions: 0 Unit cell: (68.04, 103.68, 32.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 390 8.00 N 354 7.00 C 1278 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: 0.49 Conformation dependent library (CDL) restraints added in 249.4 milliseconds 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.517A pdb=" N GLN A 15 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 15 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 17 " --> pdb=" O ILE C 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.174A pdb=" N VAL B 31 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER C 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY B 33 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 removed outlier: 5.947A pdb=" N UNK G 4 " --> pdb=" O UNK H 5 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N UNK H 4 " --> pdb=" O UNK I 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AA6, first strand: chain 'D' and resid 14 through 18 removed outlier: 5.667A pdb=" N GLN D 15 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 17 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN E 15 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE F 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 17 " --> pdb=" O ILE F 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 6.410A pdb=" N VAL D 31 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER E 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 33 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 31 " --> pdb=" O TRP F 32 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER F 34 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY E 33 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.044A pdb=" N UNK J 4 " --> pdb=" O UNK K 5 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N UNK K 4 " --> pdb=" O UNK L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 20 hydrogen bonds defined for protein. 60 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: 0.40 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 366 1.29 - 1.35: 306 1.35 - 1.42: 102 1.42 - 1.48: 324 1.48 - 1.54: 942 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.63e-01 bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.57e-01 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.45e-01 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.40e-01 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.39e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2615 1.44 - 2.89: 121 2.89 - 4.33: 6 4.33 - 5.78: 0 5.78 - 7.22: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " ideal model delta sigma weight residual 116.30 123.52 -7.22 3.50e+00 8.16e-02 4.25e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.24e+00 angle pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " ideal model delta sigma weight residual 116.30 123.50 -7.20 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.23e+00 angle pdb=" CA LEU F 38 " pdb=" CB LEU F 38 " pdb=" CG LEU F 38 " ideal model delta sigma weight residual 116.30 123.49 -7.19 3.50e+00 8.16e-02 4.22e+00 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 1052 15.81 - 31.63: 112 31.63 - 47.44: 18 47.44 - 63.26: 18 63.26 - 79.07: 6 Dihedral angle restraints: 1206 sinusoidal: 420 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLN C 15 " pdb=" CB GLN C 15 " pdb=" CG GLN C 15 " pdb=" CD GLN C 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN F 15 " pdb=" CB GLN F 15 " pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.88 37.12 3 1.50e+01 4.44e-03 6.47e+00 dihedral pdb=" CA GLN B 15 " pdb=" CB GLN B 15 " pdb=" CG GLN B 15 " pdb=" CD GLN B 15 " ideal model delta sinusoidal sigma weight residual 180.00 142.89 37.11 3 1.50e+01 4.44e-03 6.47e+00 ... (remaining 1203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 168 0.030 - 0.060: 99 0.060 - 0.091: 9 0.091 - 0.121: 42 0.121 - 0.151: 6 Chirality restraints: 324 Sorted by residual: chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CG LEU E 38 " pdb=" CB LEU E 38 " pdb=" CD1 LEU E 38 " pdb=" CD2 LEU E 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 321 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 12 " -0.010 5.00e-02 4.00e+02 1.50e-02 3.58e-01 pdb=" N PRO B 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 12 " -0.010 5.00e-02 4.00e+02 1.49e-02 3.57e-01 pdb=" N PRO E 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 12 " -0.010 5.00e-02 4.00e+02 1.48e-02 3.49e-01 pdb=" N PRO F 13 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO F 13 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO F 13 " -0.008 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 897 2.92 - 3.41: 1607 3.41 - 3.91: 3159 3.91 - 4.40: 3013 4.40 - 4.90: 6557 Nonbonded interactions: 15233 Sorted by model distance: nonbonded pdb=" ND2 ASN B 26 " pdb=" O ASN C 26 " model vdw 2.424 3.120 nonbonded pdb=" O ALA A 1 " pdb=" N ALA B 1 " model vdw 2.463 3.120 nonbonded pdb=" O ALA D 1 " pdb=" N ALA E 1 " model vdw 2.482 3.120 nonbonded pdb=" ND2 ASN D 26 " pdb=" O ASN E 26 " model vdw 2.514 3.120 nonbonded pdb=" ND2 ASN E 26 " pdb=" O ASN F 26 " model vdw 2.515 3.120 ... (remaining 15228 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 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.570 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.790 Find NCS groups from input model: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 : 0.003 0.020 2040 Z= 0.197 Angle : 0.697 7.219 2748 Z= 0.346 Chirality : 0.051 0.151 324 Planarity : 0.003 0.015 354 Dihedral : 16.942 79.069 702 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 25.81 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.57), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 32 PHE 0.003 0.002 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0694 time to fit residues: 2.5583 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN C 15 GLN E 15 GLN F 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6103 r_free = 0.6103 target = 0.447416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.6422 r_free = 0.6422 target = 0.378525 restraints weight = 2735.793| |-----------------------------------------------------------------------------| r_work (start): 0.5657 rms_B_bonded: 1.50 r_work: 0.5526 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.5428 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.5428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2040 Z= 0.235 Angle : 0.558 5.938 2748 Z= 0.282 Chirality : 0.045 0.113 324 Planarity : 0.003 0.019 354 Dihedral : 3.331 11.244 282 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.30 % Allowed : 22.04 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.55), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 32 PHE 0.003 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.213 Fit side-chains REVERT: F 24 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7582 (tt0) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0580 time to fit residues: 2.9557 Evaluate side-chains 40 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.6105 r_free = 0.6105 target = 0.447664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.6421 r_free = 0.6421 target = 0.379333 restraints weight = 2711.564| |-----------------------------------------------------------------------------| r_work (start): 0.5655 rms_B_bonded: 1.54 r_work: 0.5522 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.5423 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.5423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2040 Z= 0.189 Angle : 0.494 4.346 2748 Z= 0.255 Chirality : 0.045 0.117 324 Planarity : 0.003 0.019 354 Dihedral : 3.222 10.532 282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.45 % Allowed : 20.97 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.54), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 PHE 0.003 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.227 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 37 average time/residue: 0.1106 time to fit residues: 5.2769 Evaluate side-chains 38 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN B 26 ASN C 26 ASN D 26 ASN E 15 GLN E 26 ASN F 15 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5794 r_free = 0.5794 target = 0.240840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.191852 restraints weight = 2269.230| |-----------------------------------------------------------------------------| r_work (start): 0.5347 rms_B_bonded: 3.60 r_work: 0.5197 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.5197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 2040 Z= 0.529 Angle : 0.771 4.824 2748 Z= 0.414 Chirality : 0.050 0.129 324 Planarity : 0.005 0.030 354 Dihedral : 4.722 13.853 282 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 10.22 % Allowed : 20.97 % Favored : 68.82 % 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: -1.27 (0.52), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 32 PHE 0.004 0.001 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 33 time to evaluate : 0.230 Fit side-chains REVERT: C 24 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7780 (tt0) REVERT: E 23 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (ttpt) REVERT: F 24 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7697 (tt0) outliers start: 19 outliers final: 14 residues processed: 45 average time/residue: 0.0858 time to fit residues: 4.9217 Evaluate side-chains 46 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN D 26 ASN E 15 GLN E 26 ASN F 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6100 r_free = 0.6100 target = 0.410868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.6281 r_free = 0.6281 target = 0.374656 restraints weight = 2567.961| |-----------------------------------------------------------------------------| r_work (start): 0.5644 rms_B_bonded: 1.63 r_work: 0.5494 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.5395 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.5395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2040 Z= 0.143 Angle : 0.503 4.258 2748 Z= 0.269 Chirality : 0.045 0.118 324 Planarity : 0.003 0.022 354 Dihedral : 3.350 10.177 282 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 8.06 % Allowed : 23.66 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.51), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 32 PHE 0.004 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.233 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 41 average time/residue: 0.0660 time to fit residues: 3.7569 Evaluate side-chains 42 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.0070 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6040 r_free = 0.6040 target = 0.406128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.6237 r_free = 0.6237 target = 0.366687 restraints weight = 2571.310| |-----------------------------------------------------------------------------| r_work (start): 0.5914 rms_B_bonded: 1.65 r_work: 0.6192 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.6146 rms_B_bonded: 1.63 restraints_weight: 0.2500 r_work (final): 0.6146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2040 Z= 0.217 Angle : 0.526 3.848 2748 Z= 0.279 Chirality : 0.046 0.120 324 Planarity : 0.003 0.022 354 Dihedral : 3.566 10.992 282 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 8.06 % Allowed : 24.19 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 32 PHE 0.003 0.002 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.211 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 41 average time/residue: 0.0812 time to fit residues: 4.2869 Evaluate side-chains 45 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN D 26 ASN F 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5991 r_free = 0.5991 target = 0.399464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.6177 r_free = 0.6177 target = 0.358383 restraints weight = 2620.932| |-----------------------------------------------------------------------------| r_work (start): 0.5674 rms_B_bonded: 1.64 r_work: 0.5682 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.5618 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.5618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2040 Z= 0.360 Angle : 0.646 4.686 2748 Z= 0.346 Chirality : 0.047 0.126 324 Planarity : 0.004 0.028 354 Dihedral : 4.246 12.319 282 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 8.60 % Allowed : 23.12 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 32 PHE 0.004 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.218 Fit side-chains REVERT: A 3 LYS cc_start: 0.8025 (mptt) cc_final: 0.7344 (ttpt) outliers start: 16 outliers final: 15 residues processed: 40 average time/residue: 0.0856 time to fit residues: 4.3895 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 26 ASN D 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6024 r_free = 0.6024 target = 0.404601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.6213 r_free = 0.6213 target = 0.364147 restraints weight = 2590.456| |-----------------------------------------------------------------------------| r_work (start): 0.5716 rms_B_bonded: 1.65 r_work: 0.5735 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.5668 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.5668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2040 Z= 0.225 Angle : 0.556 4.332 2748 Z= 0.297 Chirality : 0.046 0.121 324 Planarity : 0.004 0.026 354 Dihedral : 3.744 10.768 282 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 9.68 % Allowed : 23.12 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 32 PHE 0.003 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.226 Fit side-chains REVERT: A 3 LYS cc_start: 0.7925 (mptt) cc_final: 0.7150 (tttt) outliers start: 18 outliers final: 15 residues processed: 42 average time/residue: 0.0857 time to fit residues: 4.5980 Evaluate side-chains 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.6000 r_free = 0.6000 target = 0.403483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6191 r_free = 0.6191 target = 0.362487 restraints weight = 2678.872| |-----------------------------------------------------------------------------| r_work (start): 0.5706 rms_B_bonded: 1.64 r_work: 0.5717 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.5647 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.5647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2040 Z= 0.262 Angle : 0.579 4.695 2748 Z= 0.309 Chirality : 0.046 0.122 324 Planarity : 0.003 0.024 354 Dihedral : 3.921 11.285 282 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 9.68 % Allowed : 22.04 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 32 PHE 0.003 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.241 Fit side-chains REVERT: A 3 LYS cc_start: 0.7985 (mptt) cc_final: 0.7179 (tttt) outliers start: 18 outliers final: 17 residues processed: 43 average time/residue: 0.1051 time to fit residues: 5.6009 Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.5968 r_free = 0.5968 target = 0.401300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.6173 r_free = 0.6173 target = 0.358607 restraints weight = 2587.114| |-----------------------------------------------------------------------------| r_work (start): 0.5683 rms_B_bonded: 1.61 r_work: 0.5681 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.5624 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.5624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2040 Z= 0.331 Angle : 0.618 4.306 2748 Z= 0.330 Chirality : 0.047 0.126 324 Planarity : 0.004 0.025 354 Dihedral : 4.207 11.781 282 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 10.22 % Allowed : 22.04 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 32 PHE 0.004 0.001 PHE F 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 468 Ramachandran restraints generated. 234 Oldfield, 0 Emsley, 234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.226 Fit side-chains REVERT: A 3 LYS cc_start: 0.8076 (mptt) cc_final: 0.7330 (ttpt) REVERT: C 40 GLU cc_start: 0.6856 (mp0) cc_final: 0.6654 (mp0) outliers start: 19 outliers final: 18 residues processed: 41 average time/residue: 0.0899 time to fit residues: 4.7261 Evaluate side-chains 46 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.6030 r_free = 0.6030 target = 0.441393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.6344 r_free = 0.6344 target = 0.365787 restraints weight = 2768.499| |-----------------------------------------------------------------------------| r_work (start): 0.5724 rms_B_bonded: 1.61 r_work: 0.5730 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.5662 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.5662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2040 Z= 0.219 Angle : 0.551 4.832 2748 Z= 0.294 Chirality : 0.046 0.121 324 Planarity : 0.003 0.021 354 Dihedral : 3.761 10.820 282 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.60 % Allowed : 23.66 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 32 PHE 0.003 0.001 PHE E 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1559.01 seconds wall clock time: 28 minutes 33.21 seconds (1713.21 seconds total)