Starting phenix.real_space_refine on Wed Mar 5 15:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf6_37200/03_2025/8kf6_37200.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1419 2.51 5 N 369 2.21 5 O 378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 2.98, per 1000 atoms: 1.37 Number of scatterers: 2175 At special positions: 0 Unit cell: (64.74, 95.45, 38.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 378 8.00 N 369 7.00 C 1419 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: 0.57 Conformation dependent library (CDL) restraints added in 584.1 milliseconds 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.215A pdb=" N VAL A 18 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.817A pdb=" N VAL A 40 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'G' and resid 24 through 25 removed outlier: 6.856A pdb=" N VAL G 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL H 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 10 hydrogen bonds defined for protein. 30 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: 0.46 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 705 1.34 - 1.45: 300 1.45 - 1.57: 1185 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 2208 Sorted by residual: bond pdb=" CA PHE B 20 " pdb=" C PHE B 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.37e-01 bond pdb=" CA PHE C 20 " pdb=" C PHE C 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.04e-01 bond pdb=" CA PHE A 20 " pdb=" C PHE A 20 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.34e-02 5.57e+03 8.03e-01 bond pdb=" CA VAL I 36 " pdb=" C VAL I 36 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.01e-01 bond pdb=" CB VAL A 18 " pdb=" CG2 VAL A 18 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.63e-01 ... (remaining 2203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2425 0.83 - 1.66: 421 1.66 - 2.49: 94 2.49 - 3.32: 18 3.32 - 4.15: 6 Bond angle restraints: 2964 Sorted by residual: angle pdb=" N GLU H 22 " pdb=" CA GLU H 22 " pdb=" C GLU H 22 " ideal model delta sigma weight residual 114.56 110.65 3.91 1.27e+00 6.20e-01 9.50e+00 angle pdb=" N GLY F 25 " pdb=" CA GLY F 25 " pdb=" C GLY F 25 " ideal model delta sigma weight residual 112.73 115.89 -3.16 1.20e+00 6.94e-01 6.94e+00 angle pdb=" CA GLY I 37 " pdb=" C GLY I 37 " pdb=" O GLY I 37 " ideal model delta sigma weight residual 122.39 120.13 2.26 9.30e-01 1.16e+00 5.93e+00 angle pdb=" C VAL H 12 " pdb=" N HIS H 13 " pdb=" CA HIS H 13 " ideal model delta sigma weight residual 121.80 117.65 4.15 1.71e+00 3.42e-01 5.88e+00 angle pdb=" C VAL F 24 " pdb=" N GLY F 25 " pdb=" CA GLY F 25 " ideal model delta sigma weight residual 119.98 122.37 -2.39 1.11e+00 8.12e-01 4.63e+00 ... (remaining 2959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1089 16.41 - 32.82: 123 32.82 - 49.22: 10 49.22 - 65.63: 4 65.63 - 82.04: 4 Dihedral angle restraints: 1230 sinusoidal: 444 harmonic: 786 Sorted by residual: dihedral pdb=" CA PHE C 20 " pdb=" C PHE C 20 " pdb=" N ALA C 21 " pdb=" CA ALA C 21 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE A 20 " pdb=" C PHE A 20 " pdb=" N ALA A 21 " pdb=" CA ALA A 21 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA PHE B 20 " pdb=" C PHE B 20 " pdb=" N ALA B 21 " pdb=" CA ALA B 21 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 1227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 163 0.031 - 0.062: 100 0.062 - 0.093: 18 0.093 - 0.124: 53 0.124 - 0.154: 11 Chirality restraints: 345 Sorted by residual: chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA VAL C 12 " pdb=" N VAL C 12 " pdb=" C VAL C 12 " pdb=" CB VAL C 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA VAL A 12 " pdb=" N VAL A 12 " pdb=" C VAL A 12 " pdb=" CB VAL A 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 342 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 20 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C PHE G 20 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE G 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA G 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 20 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C PHE H 20 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE H 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA H 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 20 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C PHE I 20 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE I 20 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA I 21 " 0.008 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 891 2.91 - 3.41: 1959 3.41 - 3.91: 3231 3.91 - 4.40: 3503 4.40 - 4.90: 6933 Nonbonded interactions: 16517 Sorted by model distance: nonbonded pdb=" NZ LYS I 16 " pdb=" OE2 GLU I 22 " model vdw 2.415 3.120 nonbonded pdb=" OG SER F 26 " pdb=" N ASN F 27 " model vdw 2.418 3.120 nonbonded pdb=" OG SER I 26 " pdb=" N ASN I 27 " model vdw 2.465 3.120 nonbonded pdb=" OG SER H 26 " pdb=" N ASN H 27 " model vdw 2.473 3.120 nonbonded pdb=" CE1 PHE B 20 " pdb=" CE2 PHE C 20 " model vdw 2.493 3.640 ... (remaining 16512 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 12 through 42) selection = (chain 'B' and resid 12 through 42) selection = (chain 'C' and resid 12 through 42) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 12 through 42) selection = (chain 'H' and resid 12 through 42) selection = (chain 'I' and resid 12 through 42) } 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 group one per residue 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: 1.070 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.110 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.004 0.028 2208 Z= 0.278 Angle : 0.697 4.146 2964 Z= 0.423 Chirality : 0.059 0.154 345 Planarity : 0.003 0.014 372 Dihedral : 14.133 82.040 738 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.74 (0.32), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.24), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 13 PHE 0.009 0.002 PHE G 20 TYR 0.004 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.272 Fit side-chains REVERT: F 22 GLU cc_start: 0.8574 (tp30) cc_final: 0.8367 (tp30) REVERT: I 15 GLN cc_start: 0.8750 (mp10) cc_final: 0.8473 (mp10) REVERT: B 15 GLN cc_start: 0.8911 (mp10) cc_final: 0.8463 (mp10) REVERT: C 15 GLN cc_start: 0.8738 (mp10) cc_final: 0.8394 (mp10) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1953 time to fit residues: 5.8802 Evaluate side-chains 25 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS F 15 GLN A 13 HIS G 13 HIS H 13 HIS E 13 HIS E 15 GLN I 13 HIS B 13 HIS C 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.160130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.118504 restraints weight = 2191.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.121483 restraints weight = 1356.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.123487 restraints weight = 1000.304| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2208 Z= 0.297 Angle : 0.678 6.764 2964 Z= 0.373 Chirality : 0.060 0.153 345 Planarity : 0.003 0.014 372 Dihedral : 6.107 26.726 294 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 2.28 % Allowed : 10.05 % Favored : 87.67 % 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: -5.29 (0.34), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.26), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 13 PHE 0.010 0.002 PHE A 19 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.213 Fit side-chains REVERT: I 15 GLN cc_start: 0.8689 (mp10) cc_final: 0.8448 (mp10) REVERT: B 15 GLN cc_start: 0.8885 (mp10) cc_final: 0.8609 (mp10) REVERT: C 22 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7855 (pt0) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1363 time to fit residues: 4.8326 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 10 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.176109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.132560 restraints weight = 2081.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136120 restraints weight = 1261.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.138305 restraints weight = 920.142| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2208 Z= 0.136 Angle : 0.533 5.225 2964 Z= 0.296 Chirality : 0.056 0.129 345 Planarity : 0.002 0.015 372 Dihedral : 5.671 27.706 294 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.20 % Allowed : 9.59 % Favored : 87.21 % 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: -4.68 (0.36), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.28), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.010 0.001 PHE B 20 TYR 0.004 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.239 Fit side-chains REVERT: A 22 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6673 (pp20) REVERT: E 35 MET cc_start: 0.8553 (tpp) cc_final: 0.8220 (tpp) REVERT: B 15 GLN cc_start: 0.8776 (mp10) cc_final: 0.8343 (mp10) REVERT: B 22 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6736 (pp20) REVERT: C 22 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6992 (pp20) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.1404 time to fit residues: 5.1531 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.111770 restraints weight = 2216.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.114809 restraints weight = 1366.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.116645 restraints weight = 1019.284| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2208 Z= 0.301 Angle : 0.627 5.730 2964 Z= 0.350 Chirality : 0.059 0.153 345 Planarity : 0.003 0.014 372 Dihedral : 5.860 29.743 294 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 4.11 % Allowed : 11.42 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.55 (0.37), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.28), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 13 PHE 0.014 0.002 PHE A 19 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.245 Fit side-chains REVERT: A 23 ASP cc_start: 0.7632 (m-30) cc_final: 0.7402 (m-30) REVERT: H 28 LYS cc_start: 0.8177 (mttt) cc_final: 0.7785 (mttm) REVERT: B 15 GLN cc_start: 0.8849 (mp10) cc_final: 0.8582 (mp10) REVERT: B 22 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: C 22 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6914 (pp20) outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 0.1455 time to fit residues: 5.7312 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 0.0370 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.0770 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.171500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.128512 restraints weight = 2072.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.132208 restraints weight = 1231.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.134466 restraints weight = 890.659| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2208 Z= 0.123 Angle : 0.495 4.708 2964 Z= 0.276 Chirality : 0.055 0.132 345 Planarity : 0.002 0.014 372 Dihedral : 5.397 26.817 294 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.65 % Allowed : 15.07 % Favored : 81.28 % 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: -3.96 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.011 0.001 PHE B 20 TYR 0.002 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.227 Fit side-chains REVERT: A 22 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6949 (pp20) REVERT: B 22 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: C 15 GLN cc_start: 0.8595 (mp10) cc_final: 0.8354 (mp10) REVERT: C 22 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7159 (pp20) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1368 time to fit residues: 5.1790 Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.113054 restraints weight = 2248.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.115613 restraints weight = 1472.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.117361 restraints weight = 1123.408| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2208 Z= 0.349 Angle : 0.637 5.630 2964 Z= 0.359 Chirality : 0.060 0.158 345 Planarity : 0.003 0.016 372 Dihedral : 5.798 26.406 294 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 3.65 % Allowed : 15.07 % Favored : 81.28 % 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: -4.08 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 13 PHE 0.017 0.003 PHE A 19 TYR 0.008 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.230 Fit side-chains REVERT: A 23 ASP cc_start: 0.7625 (m-30) cc_final: 0.7396 (m-30) REVERT: G 28 LYS cc_start: 0.8200 (mttt) cc_final: 0.7809 (mttp) REVERT: H 28 LYS cc_start: 0.8386 (mttt) cc_final: 0.8071 (mttp) REVERT: B 15 GLN cc_start: 0.8862 (mp10) cc_final: 0.8579 (mp10) REVERT: B 22 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: C 15 GLN cc_start: 0.8769 (mp10) cc_final: 0.8559 (mp10) REVERT: C 22 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6933 (pp20) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1560 time to fit residues: 6.4871 Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.154254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.113308 restraints weight = 2247.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.116010 restraints weight = 1438.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.117896 restraints weight = 1087.565| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2208 Z= 0.325 Angle : 0.637 5.790 2964 Z= 0.358 Chirality : 0.059 0.156 345 Planarity : 0.003 0.015 372 Dihedral : 5.954 28.832 294 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.92 % Favored : 82.08 % Rotamer: Outliers : 3.65 % Allowed : 15.07 % Favored : 81.28 % 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: -4.08 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.021 0.002 PHE H 20 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.244 Fit side-chains REVERT: E 35 MET cc_start: 0.8661 (tpp) cc_final: 0.8451 (tpp) REVERT: B 15 GLN cc_start: 0.8898 (mp10) cc_final: 0.8636 (mp10) REVERT: B 22 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6939 (pp20) REVERT: C 22 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6881 (pp20) outliers start: 8 outliers final: 6 residues processed: 33 average time/residue: 0.1315 time to fit residues: 5.2776 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.166510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.124964 restraints weight = 2185.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.127729 restraints weight = 1414.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129538 restraints weight = 1072.670| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2208 Z= 0.160 Angle : 0.538 5.199 2964 Z= 0.302 Chirality : 0.056 0.140 345 Planarity : 0.002 0.018 372 Dihedral : 5.521 28.046 294 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.65 % Allowed : 16.44 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.42), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.011 0.001 PHE B 20 TYR 0.004 0.000 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.237 Fit side-chains REVERT: A 22 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6858 (pp20) REVERT: D 22 GLU cc_start: 0.8531 (tp30) cc_final: 0.7820 (mp0) REVERT: E 35 MET cc_start: 0.8612 (tpp) cc_final: 0.8394 (tpp) REVERT: B 15 GLN cc_start: 0.8784 (mp10) cc_final: 0.8370 (mp10) REVERT: B 22 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6803 (pp20) REVERT: C 22 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7132 (pp20) outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.1288 time to fit residues: 4.8304 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 6 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 overall best weight: 2.6200 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.116040 restraints weight = 2262.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.118747 restraints weight = 1443.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.120675 restraints weight = 1087.581| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2208 Z= 0.280 Angle : 0.619 5.414 2964 Z= 0.345 Chirality : 0.058 0.154 345 Planarity : 0.002 0.016 372 Dihedral : 5.701 25.361 294 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 3.65 % Allowed : 15.53 % Favored : 80.82 % 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: -3.73 (0.43), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.013 0.002 PHE A 19 TYR 0.007 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.214 Fit side-chains REVERT: G 28 LYS cc_start: 0.8062 (mttt) cc_final: 0.7711 (mttp) REVERT: D 22 GLU cc_start: 0.8492 (tp30) cc_final: 0.7854 (mp0) REVERT: B 22 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6973 (pp20) REVERT: C 22 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6911 (pp20) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.1287 time to fit residues: 5.0065 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.162896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.121034 restraints weight = 2164.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.123788 restraints weight = 1381.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.125673 restraints weight = 1042.297| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2208 Z= 0.196 Angle : 0.559 5.171 2964 Z= 0.312 Chirality : 0.057 0.144 345 Planarity : 0.002 0.016 372 Dihedral : 5.563 25.216 294 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 3.65 % Allowed : 15.53 % Favored : 80.82 % 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: -3.67 (0.43), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 13 PHE 0.010 0.001 PHE B 20 TYR 0.005 0.001 TYR H 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 558 Ramachandran restraints generated. 279 Oldfield, 0 Emsley, 279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.236 Fit side-chains REVERT: D 22 GLU cc_start: 0.8544 (tp30) cc_final: 0.7886 (mp0) REVERT: B 22 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: C 22 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7202 (pp20) outliers start: 8 outliers final: 6 residues processed: 31 average time/residue: 0.1210 time to fit residues: 4.6800 Evaluate side-chains 31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 overall best weight: 0.7572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.173059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.130374 restraints weight = 2125.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.133565 restraints weight = 1329.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.135656 restraints weight = 989.831| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2208 Z= 0.138 Angle : 0.500 5.445 2964 Z= 0.279 Chirality : 0.055 0.136 345 Planarity : 0.002 0.016 372 Dihedral : 5.275 24.528 294 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.65 % Allowed : 15.98 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.45), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.010 0.001 PHE B 20 TYR 0.003 0.000 TYR H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1155.08 seconds wall clock time: 20 minutes 42.97 seconds (1242.97 seconds total)