Starting phenix.real_space_refine on Wed Mar 5 14:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbp_61322/03_2025/9jbp_61322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbp_61322/03_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_61322/03_2025/9jbp_61322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbp_61322/03_2025/9jbp_61322.map" model { file = "/net/cci-nas-00/data/ceres_data/9jbp_61322/03_2025/9jbp_61322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbp_61322/03_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-5624/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: 2.27, per 1000 atoms: 1.12 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: 0.48 Conformation dependent library (CDL) restraints added in 501.4 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: 0.30 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: 0.39 Time building geometry restraints manager: 0.58 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: 0.010 Normalize map: mean=0, sd=1: 1.270 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: 10.760 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:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0721 time to fit residues: 2.6268 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.6101 r_free = 0.6101 target = 0.446730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.6413 r_free = 0.6413 target = 0.377424 restraints weight = 2735.544| |-----------------------------------------------------------------------------| r_work (start): 0.5560 rms_B_bonded: 1.54 r_work: 0.5419 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.5319 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.5319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2040 Z= 0.244 Angle : 0.568 5.957 2748 Z= 0.287 Chirality : 0.045 0.115 324 Planarity : 0.004 0.020 354 Dihedral : 3.372 11.287 282 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.30 % Allowed : 22.58 % Favored : 73.12 % 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: -0.84 (0.55), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (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 41 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.172 Fit side-chains REVERT: F 24 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7583 (tt0) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0573 time to fit residues: 2.8976 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 = 0.6110 r_free = 0.6110 target = 0.451012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.6421 r_free = 0.6421 target = 0.380484 restraints weight = 2723.213| |-----------------------------------------------------------------------------| r_work (start): 0.5672 rms_B_bonded: 1.53 r_work: 0.5542 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.5446 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.5446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2040 Z= 0.171 Angle : 0.491 4.281 2748 Z= 0.252 Chirality : 0.045 0.117 324 Planarity : 0.003 0.018 354 Dihedral : 3.155 10.334 282 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.91 % Allowed : 20.97 % Favored : 73.12 % 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: -1.02 (0.54), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 45 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.212 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.0912 time to fit residues: 4.5232 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.6075 r_free = 0.6075 target = 0.404156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.6252 r_free = 0.6252 target = 0.366156 restraints weight = 2501.627| |-----------------------------------------------------------------------------| r_work (start): 0.5578 rms_B_bonded: 1.65 r_work: 0.5433 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.5337 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.5337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2040 Z= 0.266 Angle : 0.563 4.368 2748 Z= 0.295 Chirality : 0.045 0.118 324 Planarity : 0.003 0.021 354 Dihedral : 3.665 11.807 282 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 8.60 % Allowed : 22.58 % 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: -1.24 (0.51), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 32 PHE 0.003 0.001 PHE F 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 50 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.221 Fit side-chains REVERT: F 24 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7681 (tt0) outliers start: 16 outliers final: 14 residues processed: 44 average time/residue: 0.0631 time to fit residues: 3.8339 Evaluate side-chains 48 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.6111 r_free = 0.6111 target = 0.412467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6289 r_free = 0.6289 target = 0.375848 restraints weight = 2559.968| |-----------------------------------------------------------------------------| r_work (start): 0.5866 rms_B_bonded: 1.70 r_work: 0.5883 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.5815 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.5815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2040 Z= 0.139 Angle : 0.482 3.765 2748 Z= 0.255 Chirality : 0.045 0.122 324 Planarity : 0.003 0.018 354 Dihedral : 3.054 10.290 282 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 7.53 % Allowed : 23.12 % Favored : 69.35 % 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: -1.34 (0.51), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 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: 14 poor density : 33 time to evaluate : 0.214 Fit side-chains REVERT: B 14 VAL cc_start: 0.7824 (t) cc_final: 0.7420 (p) outliers start: 14 outliers final: 11 residues processed: 40 average time/residue: 0.0705 time to fit residues: 3.8046 Evaluate side-chains 40 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 VAL 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: 0.0050 chunk 11 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.6126 r_free = 0.6126 target = 0.455381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.6435 r_free = 0.6435 target = 0.384937 restraints weight = 2731.948| |-----------------------------------------------------------------------------| r_work (start): 0.6021 rms_B_bonded: 1.54 r_work: 0.6273 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.6231 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.6231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2040 Z= 0.120 Angle : 0.467 4.819 2748 Z= 0.244 Chirality : 0.045 0.115 324 Planarity : 0.003 0.016 354 Dihedral : 2.851 9.786 282 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 7.53 % Allowed : 24.19 % 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: -1.39 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 32 PHE 0.005 0.001 PHE E 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 43 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.225 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 36 average time/residue: 0.0639 time to fit residues: 3.2809 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 15 GLN C 26 ASN D 26 ASN 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 = 0.5806 r_free = 0.5806 target = 0.243006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.192634 restraints weight = 2323.539| |-----------------------------------------------------------------------------| r_work (start): 0.5355 rms_B_bonded: 3.60 r_work: 0.5208 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.5208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 2040 Z= 0.519 Angle : 0.738 4.897 2748 Z= 0.398 Chirality : 0.050 0.127 324 Planarity : 0.004 0.029 354 Dihedral : 4.685 13.581 282 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 8.60 % Allowed : 25.27 % Favored : 66.13 % 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: -1.58 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 32 PHE 0.006 0.002 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 49 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 33 time to evaluate : 0.193 Fit side-chains REVERT: C 24 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7783 (tt0) REVERT: F 24 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7891 (tt0) outliers start: 16 outliers final: 15 residues processed: 44 average time/residue: 0.0616 time to fit residues: 3.7441 Evaluate side-chains 45 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 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 29 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain D residue 25 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6060 r_free = 0.6060 target = 0.407781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.6243 r_free = 0.6243 target = 0.368667 restraints weight = 2569.368| |-----------------------------------------------------------------------------| r_work (start): 0.5758 rms_B_bonded: 1.69 r_work: 0.5771 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.5704 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.5704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2040 Z= 0.161 Angle : 0.520 4.591 2748 Z= 0.277 Chirality : 0.045 0.122 324 Planarity : 0.003 0.027 354 Dihedral : 3.460 11.269 282 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 8.06 % Allowed : 25.27 % Favored : 66.67 % 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: -1.53 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 32 PHE 0.004 0.001 PHE E 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 47 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.210 Fit side-chains REVERT: A 3 LYS cc_start: 0.7847 (mptt) cc_final: 0.7119 (tttt) REVERT: B 14 VAL cc_start: 0.8569 (p) cc_final: 0.8310 (t) outliers start: 15 outliers final: 15 residues processed: 39 average time/residue: 0.0715 time to fit residues: 3.7270 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 : 0.192 ------------------------------------------------------------------------------- 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 C 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.6013 r_free = 0.6013 target = 0.404242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.6207 r_free = 0.6207 target = 0.363126 restraints weight = 2653.297| |-----------------------------------------------------------------------------| r_work (start): 0.5712 rms_B_bonded: 1.69 r_work: 0.5733 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.5665 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.5665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2040 Z= 0.232 Angle : 0.554 5.101 2748 Z= 0.296 Chirality : 0.046 0.122 324 Planarity : 0.003 0.027 354 Dihedral : 3.678 11.858 282 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 8.60 % Allowed : 25.81 % Favored : 65.59 % 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: -1.64 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 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 44 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.216 Fit side-chains REVERT: A 3 LYS cc_start: 0.7907 (mptt) cc_final: 0.7201 (tttt) outliers start: 16 outliers final: 14 residues processed: 38 average time/residue: 0.0789 time to fit residues: 4.0858 Evaluate side-chains 42 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.5994 r_free = 0.5994 target = 0.402572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.6191 r_free = 0.6191 target = 0.360971 restraints weight = 2550.133| |-----------------------------------------------------------------------------| r_work (start): 0.5696 rms_B_bonded: 1.66 r_work: 0.5708 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.5645 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.5645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2040 Z= 0.259 Angle : 0.567 4.341 2748 Z= 0.303 Chirality : 0.046 0.125 324 Planarity : 0.003 0.029 354 Dihedral : 3.867 12.123 282 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.06 % Allowed : 26.34 % Favored : 65.59 % 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: -1.74 (0.49), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 32 PHE 0.003 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: 15 poor density : 32 time to evaluate : 0.203 Fit side-chains REVERT: A 3 LYS cc_start: 0.7973 (mptt) cc_final: 0.7185 (tttt) outliers start: 15 outliers final: 15 residues processed: 39 average time/residue: 0.0694 time to fit residues: 3.6317 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 : 0.203 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.6048 r_free = 0.6048 target = 0.408304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.6240 r_free = 0.6240 target = 0.367938 restraints weight = 2578.034| |-----------------------------------------------------------------------------| r_work (start): 0.5760 rms_B_bonded: 1.70 r_work: 0.5777 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.5708 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.5708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3051 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= 0.160 Angle : 0.513 4.822 2748 Z= 0.274 Chirality : 0.045 0.119 324 Planarity : 0.003 0.025 354 Dihedral : 3.355 11.009 282 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 7.53 % Allowed : 26.88 % Favored : 65.59 % 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: -1.64 (0.50), residues: 234 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 32 PHE 0.004 0.001 PHE B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.41 seconds wall clock time: 27 minutes 25.49 seconds (1645.49 seconds total)