Starting phenix.real_space_refine on Thu Oct 22 17:37:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7j_72301/10_2026/9q7j_72301.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1512 2.51 5 N 549 2.21 5 O 432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2493 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 277 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 0.48, per 1000 atoms: 0.19 Number of scatterers: 2493 At special positions: 0 Unit cell: (101.088, 94.536, 31.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 432 8.00 N 549 7.00 C 1512 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: 0.16 Conformation dependent library (CDL) restraints added in 113.3 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.650A pdb=" N GLN B 28 " --> pdb=" O GLN E 29 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN E 28 " --> pdb=" O GLN H 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 12 removed outlier: 6.421A pdb=" N GLN C 9 " --> pdb=" O GLN F 10 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU F 12 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS C 11 " --> pdb=" O LEU F 12 " (cutoff:3.500A) 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: 0.17 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 423 1.29 - 1.36: 603 1.36 - 1.42: 189 1.42 - 1.49: 282 1.49 - 1.56: 1059 Bond restraints: 2556 Sorted by residual: bond pdb=" CB GLN I 10 " pdb=" CG GLN I 10 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CB GLN F 10 " pdb=" CG GLN F 10 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CB GLN C 10 " pdb=" CG GLN C 10 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" CG LEU G 2 " pdb=" CD1 LEU G 2 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.71e-01 bond pdb=" CG LEU A 2 " pdb=" CD1 LEU A 2 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.71e-01 ... (remaining 2551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 3241 1.45 - 2.90: 167 2.90 - 4.35: 12 4.35 - 5.80: 12 5.80 - 7.25: 6 Bond angle restraints: 3438 Sorted by residual: angle pdb=" CA GLN C 8 " pdb=" CB GLN C 8 " pdb=" CG GLN C 8 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" N GLN H 9 " pdb=" CA GLN H 9 " pdb=" C GLN H 9 " ideal model delta sigma weight residual 109.71 105.00 4.71 1.41e+00 5.03e-01 1.12e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" C GLN B 9 " ideal model delta sigma weight residual 109.71 105.00 4.71 1.41e+00 5.03e-01 1.12e+01 angle pdb=" CA GLN F 8 " pdb=" CB GLN F 8 " pdb=" CG GLN F 8 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLN I 8 " pdb=" CB GLN I 8 " pdb=" CG GLN I 8 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.11e+01 ... (remaining 3433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1185 16.00 - 32.00: 234 32.00 - 48.00: 42 48.00 - 64.01: 33 64.01 - 80.01: 9 Dihedral angle restraints: 1503 sinusoidal: 675 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN A 8 " pdb=" C GLN A 8 " pdb=" N GLN A 9 " pdb=" CA GLN A 9 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN G 8 " pdb=" C GLN G 8 " pdb=" N GLN G 9 " pdb=" CA GLN G 9 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN D 8 " pdb=" C GLN D 8 " pdb=" N GLN D 9 " pdb=" CA GLN D 9 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 1500 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 178 0.027 - 0.052: 75 0.052 - 0.078: 53 0.078 - 0.104: 12 0.104 - 0.129: 15 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA VAL H 15 " pdb=" N VAL H 15 " pdb=" C VAL H 15 " pdb=" CB VAL H 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA VAL E 15 " pdb=" N VAL E 15 " pdb=" C VAL E 15 " pdb=" CB VAL E 15 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA VAL A 21 " pdb=" N VAL A 21 " pdb=" C VAL A 21 " pdb=" CB VAL A 21 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 330 not shown) Planarity restraints: 486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 26 " 0.007 2.00e-02 2.50e+03 7.39e-03 8.20e-01 pdb=" CG HIS E 26 " -0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS E 26 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS E 26 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS E 26 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 26 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 26 " 0.007 2.00e-02 2.50e+03 7.26e-03 7.90e-01 pdb=" CG HIS B 26 " -0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS B 26 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 26 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 26 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 26 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 26 " 0.007 2.00e-02 2.50e+03 7.25e-03 7.89e-01 pdb=" CG HIS H 26 " -0.016 2.00e-02 2.50e+03 pdb=" ND1 HIS H 26 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS H 26 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS H 26 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS H 26 " 0.003 2.00e-02 2.50e+03 ... (remaining 483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 507 2.79 - 3.32: 2334 3.32 - 3.85: 3807 3.85 - 4.37: 4338 4.37 - 4.90: 8052 Nonbonded interactions: 19038 Sorted by model distance: nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.263 3.040 nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.263 3.040 nonbonded pdb=" O SER G 31 " pdb=" OG SER G 31 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLN B 4 " pdb=" NE2 GLN B 6 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLN H 4 " pdb=" NE2 GLN H 6 " model vdw 2.313 3.120 ... (remaining 19033 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.760 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5175 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 0.035 2556 Z= 0.204 Angle : 0.779 7.251 3438 Z= 0.434 Chirality : 0.045 0.129 333 Planarity : 0.002 0.009 486 Dihedral : 20.198 80.007 945 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 26.88 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.41), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE B 23 HIS 0.008 0.002 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 ( 2556) covalent geometry : angle 0.77856 / 0.43 ( 3438) hydrogen bonds : bond 0.25055 / 12.66 ( 10) hydrogen bonds : angle 6.92001 / 4.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.049 Fit side-chains REVERT: A 25 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 29 GLN cc_start: 0.6151 (tt0) cc_final: 0.5894 (tm-30) REVERT: E 29 GLN cc_start: 0.6264 (tt0) cc_final: 0.5971 (tm-30) REVERT: I 8 GLN cc_start: 0.5491 (tm-30) cc_final: 0.4883 (pt0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0232 time to fit residues: 1.4114 Evaluate side-chains 30 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [12, 24, 13, 1, 8, 16, 15, 25, 26, 9, 11] chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** H 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 27 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5379 r_free = 0.5379 target = 0.282396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.155517 restraints weight = 2958.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.156787 restraints weight = 2240.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.157471 restraints weight = 1879.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.157504 restraints weight = 1701.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.158759 restraints weight = 1688.816| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2556 Z= 0.224 Angle : 0.801 8.799 3438 Z= 0.423 Chirality : 0.046 0.154 333 Planarity : 0.003 0.011 486 Dihedral : 7.809 22.884 270 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 3.23 % Allowed : 24.01 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.004 PHE G 23 HIS 0.012 0.002 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 2556) covalent geometry : angle 0.80110 / 0.42 ( 3438) hydrogen bonds : bond 0.03710 / 1.94 ( 10) hydrogen bonds : angle 4.73052 / 3.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.055 Fit side-chains REVERT: C 5 GLN cc_start: 0.7533 (tp40) cc_final: 0.7325 (mm-40) REVERT: E 7 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7088 (m170) REVERT: F 5 GLN cc_start: 0.7380 (tp40) cc_final: 0.6917 (mm-40) REVERT: F 25 GLN cc_start: 0.8103 (mt0) cc_final: 0.7419 (mp10) REVERT: G 12 LEU cc_start: 0.8076 (mp) cc_final: 0.7841 (mp) REVERT: H 7 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6488 (m170) REVERT: I 5 GLN cc_start: 0.7599 (tp40) cc_final: 0.7093 (tm-30) outliers start: 9 outliers final: 2 residues processed: 33 average time/residue: 0.0228 time to fit residues: 1.0308 Evaluate side-chains 23 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain H residue 7 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [15, 21, 6, 5, 11, 17, 26, 22, 14, 12, 10] chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 6 GLN B 11 HIS ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 29 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 3 HIS ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5396 r_free = 0.5396 target = 0.286893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5252 r_free = 0.5252 target = 0.156287 restraints weight = 2953.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.157462 restraints weight = 2293.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.158538 restraints weight = 1953.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.158538 restraints weight = 1768.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.158538 restraints weight = 1768.706| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2556 Z= 0.198 Angle : 0.714 8.993 3438 Z= 0.375 Chirality : 0.044 0.148 333 Planarity : 0.003 0.009 486 Dihedral : 7.339 20.878 270 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 2.87 % Allowed : 29.75 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.003 PHE A 23 HIS 0.010 0.002 HIS I 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 2556) covalent geometry : angle 0.71366 / 0.38 ( 3438) hydrogen bonds : bond 0.02752 / 1.48 ( 10) hydrogen bonds : angle 4.45468 / 2.77 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.055 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: F 25 GLN cc_start: 0.8071 (mt0) cc_final: 0.7429 (mp10) REVERT: G 12 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7903 (mp) outliers start: 8 outliers final: 3 residues processed: 27 average time/residue: 0.0259 time to fit residues: 0.9806 Evaluate side-chains 24 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [26, 10, 4, 22, 17, 11, 18, 5, 2, 7, 3] chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS G 28 GLN H 6 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.153800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.101543 restraints weight = 3227.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.099822 restraints weight = 3199.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.101332 restraints weight = 2513.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.101817 restraints weight = 1974.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.102016 restraints weight = 1857.635| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2556 Z= 0.175 Angle : 0.652 7.328 3438 Z= 0.344 Chirality : 0.043 0.145 333 Planarity : 0.002 0.009 486 Dihedral : 7.055 19.813 270 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 2.87 % Allowed : 31.54 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.39), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE A 23 HIS 0.008 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 2556) covalent geometry : angle 0.65235 / 0.34 ( 3438) hydrogen bonds : bond 0.02490 / 1.36 ( 10) hydrogen bonds : angle 4.29464 / 2.63 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: F 25 GLN cc_start: 0.8048 (mt0) cc_final: 0.7397 (mp10) REVERT: G 12 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7856 (mp) outliers start: 8 outliers final: 3 residues processed: 26 average time/residue: 0.0346 time to fit residues: 1.3089 Evaluate side-chains 23 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [20, 10, 12, 11, 3, 17, 24, 4, 19, 15, 18] chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN B 3 HIS ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5427 r_free = 0.5427 target = 0.292280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.159591 restraints weight = 2929.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.160734 restraints weight = 2238.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.161401 restraints weight = 1931.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.161401 restraints weight = 1747.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.161401 restraints weight = 1747.882| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2556 Z= 0.155 Angle : 0.612 6.928 3438 Z= 0.326 Chirality : 0.042 0.142 333 Planarity : 0.002 0.008 486 Dihedral : 6.770 18.679 270 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 2.51 % Allowed : 33.33 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.39), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE A 23 HIS 0.007 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 2556) covalent geometry : angle 0.61241 / 0.33 ( 3438) hydrogen bonds : bond 0.02305 / 1.25 ( 10) hydrogen bonds : angle 4.21056 / 2.57 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.092 Fit side-chains REVERT: E 11 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6238 (t-90) REVERT: F 25 GLN cc_start: 0.8055 (mt0) cc_final: 0.7425 (mp10) REVERT: G 12 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8008 (mp) REVERT: I 5 GLN cc_start: 0.7753 (tp40) cc_final: 0.7306 (tm-30) outliers start: 7 outliers final: 3 residues processed: 23 average time/residue: 0.0298 time to fit residues: 0.9878 Evaluate side-chains 22 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [21, 22, 13, 15, 10, 23, 18, 5, 7, 11, 19] chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 6 GLN ** E 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 29 GLN ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.153973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.101737 restraints weight = 3201.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.099878 restraints weight = 3197.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.102069 restraints weight = 2488.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.101929 restraints weight = 1920.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.102040 restraints weight = 1837.294| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2556 Z= 0.174 Angle : 0.616 6.704 3438 Z= 0.334 Chirality : 0.042 0.144 333 Planarity : 0.002 0.009 486 Dihedral : 6.816 19.262 270 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Rotamer: Outliers : 2.87 % Allowed : 34.41 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.39), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.003 PHE A 23 HIS 0.009 0.001 HIS E 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 2556) covalent geometry : angle 0.61595 / 0.33 ( 3438) hydrogen bonds : bond 0.02376 / 1.29 ( 10) hydrogen bonds : angle 4.26854 / 2.54 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: F 25 GLN cc_start: 0.7963 (mt0) cc_final: 0.7283 (mp10) REVERT: G 12 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7789 (mp) REVERT: G 17 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.1904 (p-80) outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.0343 time to fit residues: 1.1924 Evaluate side-chains 23 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [3, 0, 24, 22, 25, 12, 13, 8, 10, 16, 17] chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 11 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.153135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.101852 restraints weight = 3413.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.103771 restraints weight = 2433.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.105112 restraints weight = 1923.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.105904 restraints weight = 1635.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.106511 restraints weight = 1471.786| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2556 Z= 0.231 Angle : 0.683 7.187 3438 Z= 0.376 Chirality : 0.044 0.149 333 Planarity : 0.003 0.013 486 Dihedral : 7.303 20.390 270 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.07 % Favored : 78.93 % Rotamer: Outliers : 3.23 % Allowed : 35.13 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE A 23 HIS 0.012 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 ( 2556) covalent geometry : angle 0.68331 / 0.38 ( 3438) hydrogen bonds : bond 0.02667 / 1.48 ( 10) hydrogen bonds : angle 4.64072 / 2.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.094 Fit side-chains REVERT: E 11 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.6224 (t-90) REVERT: F 25 GLN cc_start: 0.8057 (mt0) cc_final: 0.7322 (mp10) REVERT: G 12 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7931 (mp) REVERT: G 17 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5271 (t-90) REVERT: I 5 GLN cc_start: 0.7769 (tp40) cc_final: 0.7261 (tm-30) outliers start: 9 outliers final: 4 residues processed: 23 average time/residue: 0.0260 time to fit residues: 0.8917 Evaluate side-chains 23 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [17, 6, 13, 7, 24, 18, 3, 20, 14, 19, 2] chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 24 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS F 9 GLN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5419 r_free = 0.5419 target = 0.291381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5286 r_free = 0.5286 target = 0.157141 restraints weight = 2970.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.157996 restraints weight = 2302.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.158617 restraints weight = 2003.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.158618 restraints weight = 1840.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.158618 restraints weight = 1839.500| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2556 Z= 0.183 Angle : 0.635 6.977 3438 Z= 0.346 Chirality : 0.043 0.144 333 Planarity : 0.002 0.010 486 Dihedral : 6.987 19.672 270 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.56 % Favored : 85.44 % Rotamer: Outliers : 2.87 % Allowed : 36.20 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE A 23 HIS 0.008 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 2556) covalent geometry : angle 0.63488 / 0.35 ( 3438) hydrogen bonds : bond 0.02404 / 1.34 ( 10) hydrogen bonds : angle 4.57783 / 2.62 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.056 Fit side-chains REVERT: E 11 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.6318 (t-90) REVERT: F 25 GLN cc_start: 0.8029 (mt0) cc_final: 0.7294 (mp10) REVERT: G 12 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7980 (mp) REVERT: G 17 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5326 (t-90) REVERT: I 5 GLN cc_start: 0.7764 (tp40) cc_final: 0.7335 (tm-30) REVERT: I 24 HIS cc_start: 0.7397 (t70) cc_final: 0.6667 (m90) outliers start: 8 outliers final: 4 residues processed: 22 average time/residue: 0.0361 time to fit residues: 1.1438 Evaluate side-chains 21 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [7, 1, 0, 11, 6, 26, 22, 15, 25, 17, 23] chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5431 r_free = 0.5431 target = 0.293105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.158473 restraints weight = 2981.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.159470 restraints weight = 2336.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.160056 restraints weight = 2007.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.160934 restraints weight = 1822.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.160934 restraints weight = 1711.832| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2556 Z= 0.165 Angle : 0.615 6.932 3438 Z= 0.331 Chirality : 0.042 0.140 333 Planarity : 0.002 0.009 486 Dihedral : 6.767 19.447 270 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 2.87 % Allowed : 35.48 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE D 23 HIS 0.007 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 2556) covalent geometry : angle 0.61535 / 0.33 ( 3438) hydrogen bonds : bond 0.02262 / 1.25 ( 10) hydrogen bonds : angle 4.54428 / 2.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.151 Fit side-chains REVERT: E 11 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.6202 (t-90) REVERT: F 25 GLN cc_start: 0.8018 (mt0) cc_final: 0.7253 (mp10) REVERT: G 12 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7946 (mp) REVERT: G 17 HIS cc_start: 0.6031 (OUTLIER) cc_final: 0.5335 (t-90) REVERT: I 5 GLN cc_start: 0.7771 (tp40) cc_final: 0.7348 (tm-30) outliers start: 8 outliers final: 4 residues processed: 21 average time/residue: 0.0329 time to fit residues: 1.0622 Evaluate side-chains 22 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 11 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [22, 8, 10, 4, 13, 3, 23, 14, 26, 12, 24] chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 29 GLN ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5450 r_free = 0.5450 target = 0.294840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.160232 restraints weight = 2988.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.161324 restraints weight = 2290.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.161825 restraints weight = 1911.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.161825 restraints weight = 1764.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.161825 restraints weight = 1764.819| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2556 Z= 0.152 Angle : 0.604 7.200 3438 Z= 0.323 Chirality : 0.042 0.138 333 Planarity : 0.002 0.007 486 Dihedral : 6.640 21.354 270 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 2.15 % Allowed : 35.84 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.40), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE D 23 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 2556) covalent geometry : angle 0.60403 / 0.32 ( 3438) hydrogen bonds : bond 0.02122 / 1.16 ( 10) hydrogen bonds : angle 4.48131 / 2.56 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.099 Fit side-chains REVERT: F 25 GLN cc_start: 0.7995 (mt0) cc_final: 0.7288 (mp10) REVERT: G 12 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7895 (mp) REVERT: G 17 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5426 (t-90) REVERT: I 5 GLN cc_start: 0.7789 (tp40) cc_final: 0.7375 (tm-30) outliers start: 6 outliers final: 4 residues processed: 19 average time/residue: 0.0365 time to fit residues: 1.0405 Evaluate side-chains 21 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain I residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [26, 10, 12, 9, 20, 4, 8, 0, 2, 17, 16] chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.0060 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 HIS ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 11 HIS ** I 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.299980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.5411 r_free = 0.5411 target = 0.167892 restraints weight = 2956.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.165769 restraints weight = 2985.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.165825 restraints weight = 2700.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.165854 restraints weight = 2643.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.165854 restraints weight = 2623.248| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2556 Z= 0.122 Angle : 0.562 7.045 3438 Z= 0.298 Chirality : 0.041 0.130 333 Planarity : 0.002 0.006 486 Dihedral : 6.152 20.637 270 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.58 % Allowed : 34.77 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.39), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 23 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 2556) covalent geometry : angle 0.56236 / 0.30 ( 3438) hydrogen bonds : bond 0.01818 / 1.01 ( 10) hydrogen bonds : angle 4.36150 / 2.53 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 682.96 seconds wall clock time: 12 minutes 28.15 seconds (748.15 seconds total)