Starting phenix.real_space_refine on Wed Nov 13 23:26:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_37200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_37200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_37200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_37200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf6_37200/11_2024/8kf6_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.13, per 1000 atoms: 0.98 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: 0.48 Conformation dependent library (CDL) restraints added in 260.8 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: 0.26 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: 0.37 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 - 1.34: 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.100 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- 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 : 0.203 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: 0.1484 time to fit residues: 4.5009 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 : 0.229 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.207 Fit side-chains REVERT: F 35 MET cc_start: 0.7643 (ttm) cc_final: 0.7385 (ttp) REVERT: I 15 GLN cc_start: 0.8738 (mp10) cc_final: 0.8378 (mp10) REVERT: B 15 GLN cc_start: 0.8883 (mp10) cc_final: 0.8498 (mp10) REVERT: C 15 GLN cc_start: 0.8766 (mp10) cc_final: 0.8560 (mp10) REVERT: C 22 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7841 (pt0) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1359 time to fit residues: 4.8090 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 13 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2208 Z= 0.206 Angle : 0.584 5.515 2964 Z= 0.324 Chirality : 0.058 0.142 345 Planarity : 0.002 0.015 372 Dihedral : 5.810 28.530 294 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer: Outliers : 4.11 % Allowed : 10.96 % Favored : 84.93 % 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: -4.88 (0.35), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.27), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.010 0.002 PHE B 20 TYR 0.006 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 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.235 Fit side-chains REVERT: F 22 GLU cc_start: 0.8610 (tp30) cc_final: 0.8402 (tp30) REVERT: F 35 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7214 (ttm) REVERT: B 15 GLN cc_start: 0.8832 (mp10) cc_final: 0.8422 (mp10) REVERT: B 22 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6839 (pp20) REVERT: C 15 GLN cc_start: 0.8740 (mp10) cc_final: 0.8523 (mp10) REVERT: C 22 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.6872 (pp20) outliers start: 9 outliers final: 6 residues processed: 30 average time/residue: 0.1392 time to fit residues: 5.1268 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2208 Z= 0.256 Angle : 0.599 5.754 2964 Z= 0.335 Chirality : 0.059 0.150 345 Planarity : 0.002 0.014 372 Dihedral : 5.823 29.207 294 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 4.11 % Allowed : 12.79 % Favored : 83.11 % 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: -4.56 (0.37), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.28), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.011 0.002 PHE B 20 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 32 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.312 Fit side-chains REVERT: F 22 GLU cc_start: 0.8620 (tp30) cc_final: 0.8375 (tp30) REVERT: F 35 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7208 (ttm) REVERT: A 23 ASP cc_start: 0.7619 (m-30) cc_final: 0.7383 (m-30) REVERT: D 35 MET cc_start: 0.8650 (mmm) cc_final: 0.8165 (ttm) REVERT: B 15 GLN cc_start: 0.8833 (mp10) cc_final: 0.8436 (mp10) REVERT: B 22 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6852 (pp20) REVERT: C 15 GLN cc_start: 0.8755 (mp10) cc_final: 0.8516 (mp10) REVERT: C 22 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6918 (pp20) outliers start: 9 outliers final: 6 residues processed: 29 average time/residue: 0.1259 time to fit residues: 4.5524 Evaluate side-chains 33 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 MET 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 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.0270 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2352 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= 0.120 Angle : 0.482 4.708 2964 Z= 0.270 Chirality : 0.055 0.128 345 Planarity : 0.002 0.015 372 Dihedral : 5.338 26.533 294 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.11 % Allowed : 14.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.009 0.001 PHE B 20 TYR 0.003 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: 9 poor density : 23 time to evaluate : 0.239 Fit side-chains REVERT: A 22 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: D 22 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: D 35 MET cc_start: 0.8524 (mmm) cc_final: 0.8184 (ttm) REVERT: E 35 MET cc_start: 0.8585 (tpp) cc_final: 0.8238 (tpp) REVERT: B 22 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: C 15 GLN cc_start: 0.8554 (mp10) cc_final: 0.8331 (mp10) REVERT: C 22 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7163 (pp20) outliers start: 9 outliers final: 4 residues processed: 29 average time/residue: 0.1315 time to fit residues: 4.7394 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 : 0.234 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 6 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2208 Z= 0.367 Angle : 0.648 5.747 2964 Z= 0.364 Chirality : 0.060 0.160 345 Planarity : 0.003 0.016 372 Dihedral : 5.791 26.210 294 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 4.11 % Allowed : 13.70 % Favored : 82.19 % 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: -4.06 (0.40), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 13 PHE 0.019 0.003 PHE H 20 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: 9 poor density : 28 time to evaluate : 0.224 Fit side-chains REVERT: G 28 LYS cc_start: 0.8056 (mttt) cc_final: 0.7686 (mttp) REVERT: D 22 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: D 35 MET cc_start: 0.8671 (mmm) cc_final: 0.8121 (ttm) REVERT: H 28 LYS cc_start: 0.8129 (mttt) cc_final: 0.7766 (mttp) REVERT: I 28 LYS cc_start: 0.8352 (mttt) cc_final: 0.8081 (mttp) REVERT: B 15 GLN cc_start: 0.8870 (mp10) cc_final: 0.8406 (mp10) REVERT: C 15 GLN cc_start: 0.8733 (mp10) cc_final: 0.8499 (mp10) REVERT: C 22 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6868 (pp20) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1659 time to fit residues: 6.6515 Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 15 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2208 Z= 0.249 Angle : 0.579 5.682 2964 Z= 0.325 Chirality : 0.058 0.149 345 Planarity : 0.002 0.016 372 Dihedral : 5.752 28.855 294 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.57 % Allowed : 13.70 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.41), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.018 0.002 PHE H 20 TYR 0.006 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 36 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.235 Fit side-chains REVERT: D 22 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: B 15 GLN cc_start: 0.8855 (mp10) cc_final: 0.8378 (mp10) REVERT: B 22 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6893 (pp20) REVERT: C 15 GLN cc_start: 0.8698 (mp10) cc_final: 0.8478 (mp10) REVERT: C 22 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6782 (pp20) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 0.1220 time to fit residues: 4.8418 Evaluate side-chains 35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 22 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2208 Z= 0.277 Angle : 0.594 5.610 2964 Z= 0.334 Chirality : 0.058 0.153 345 Planarity : 0.003 0.017 372 Dihedral : 5.731 28.358 294 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 4.11 % Allowed : 14.61 % 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: -3.89 (0.42), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.015 0.002 PHE B 20 TYR 0.007 0.001 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 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.241 Fit side-chains REVERT: G 28 LYS cc_start: 0.7974 (mttt) cc_final: 0.7574 (mttp) REVERT: D 22 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: D 35 MET cc_start: 0.8648 (mmm) cc_final: 0.7967 (ttm) REVERT: H 28 LYS cc_start: 0.8052 (mttt) cc_final: 0.7617 (mttp) REVERT: B 15 GLN cc_start: 0.8851 (mp10) cc_final: 0.8372 (mp10) REVERT: B 22 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6911 (pp20) REVERT: C 15 GLN cc_start: 0.8719 (mp10) cc_final: 0.8492 (mp10) REVERT: C 22 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.6784 (pp20) outliers start: 9 outliers final: 6 residues processed: 34 average time/residue: 0.1556 time to fit residues: 6.3207 Evaluate side-chains 37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 26 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2208 Z= 0.294 Angle : 0.606 5.762 2964 Z= 0.341 Chirality : 0.058 0.153 345 Planarity : 0.003 0.017 372 Dihedral : 5.801 28.067 294 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % Rotamer: Outliers : 4.11 % Allowed : 14.16 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.43), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 13 PHE 0.018 0.002 PHE H 20 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: 9 poor density : 25 time to evaluate : 0.238 Fit side-chains REVERT: D 22 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 15 GLN cc_start: 0.8882 (mp10) cc_final: 0.8391 (mp10) REVERT: B 22 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: C 15 GLN cc_start: 0.8746 (mp10) cc_final: 0.8524 (mp10) REVERT: C 22 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7365 (pp20) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.1203 time to fit residues: 4.6481 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 5 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2208 Z= 0.197 Angle : 0.550 5.388 2964 Z= 0.307 Chirality : 0.057 0.146 345 Planarity : 0.002 0.016 372 Dihedral : 5.517 25.467 294 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.11 % Allowed : 14.61 % 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: -3.63 (0.44), residues: 279 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 13 PHE 0.013 0.001 PHE H 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 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.231 Fit side-chains REVERT: D 22 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: D 35 MET cc_start: 0.8599 (mmm) cc_final: 0.7863 (ttm) REVERT: B 15 GLN cc_start: 0.8807 (mp10) cc_final: 0.8306 (mp10) REVERT: B 22 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: C 15 GLN cc_start: 0.8724 (mp10) cc_final: 0.8501 (mp10) REVERT: C 22 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6828 (pp20) outliers start: 9 outliers final: 6 residues processed: 31 average time/residue: 0.1307 time to fit residues: 4.9816 Evaluate side-chains 34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 D residue 22 GLU 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 18 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 3 optimal weight: 10.0000 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4310 r_free = 0.4310 target = 0.156223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.114882 restraints weight = 2198.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.117670 restraints weight = 1386.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.119565 restraints weight = 1041.020| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2208 Z= 0.275 Angle : 0.596 5.601 2964 Z= 0.333 Chirality : 0.058 0.153 345 Planarity : 0.002 0.016 372 Dihedral : 5.656 25.557 294 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 4.57 % Allowed : 14.16 % 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: -3.67 (0.44), 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 0.005 0.001 HIS B 13 PHE 0.016 0.002 PHE H 20 TYR 0.006 0.001 TYR H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 944.53 seconds wall clock time: 17 minutes 43.53 seconds (1063.53 seconds total)