Starting phenix.real_space_refine on Sun Apr 27 00:19:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.map" model { file = "/net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ft7_50741/04_2025/9ft7_50741.cif" } resolution = 3.16 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= 0.001 sd= 0.043 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 22 5.16 5 C 2656 2.51 5 N 652 2.21 5 O 684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4016 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1987 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' K': 2, 'EIC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 3.44, per 1000 atoms: 0.86 Number of scatterers: 4016 At special positions: 0 Unit cell: (80.704, 69.056, 93.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 22 16.00 O 684 8.00 N 652 7.00 C 2656 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: 1.14 Conformation dependent library (CDL) restraints added in 469.5 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 14 through 64 removed outlier: 3.746A pdb=" N ALA A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.519A pdb=" N ILE A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 294 Processing helix chain 'B' and resid 15 through 64 removed outlier: 3.746A pdb=" N ALA B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 164 removed outlier: 3.519A pdb=" N ILE B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 294 347 hydrogen bonds defined for protein. 1041 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: 1.06 Time building geometry restraints manager: 1.29 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: 1234 1.34 - 1.46: 709 1.46 - 1.57: 2137 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 4110 Sorted by residual: bond pdb=" CB THR A 116 " pdb=" CG2 THR A 116 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CB THR B 116 " pdb=" CG2 THR B 116 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00 bond pdb=" CB THR B 138 " pdb=" CG2 THR B 138 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 138 " pdb=" CG2 THR A 138 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.36e+00 bond pdb=" C1 EIC B 401 " pdb=" C2 EIC B 401 " ideal model delta sigma weight residual 1.539 1.516 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 4105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 4990 1.01 - 2.02: 480 2.02 - 3.02: 78 3.02 - 4.03: 22 4.03 - 5.04: 2 Bond angle restraints: 5572 Sorted by residual: angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" C GLU B 42 " ideal model delta sigma weight residual 112.54 115.62 -3.08 1.51e+00 4.39e-01 4.15e+00 angle pdb=" N GLU A 42 " pdb=" CA GLU A 42 " pdb=" C GLU A 42 " ideal model delta sigma weight residual 112.54 115.62 -3.08 1.51e+00 4.39e-01 4.15e+00 angle pdb=" C PHE A 142 " pdb=" N ASN A 143 " pdb=" CA ASN A 143 " ideal model delta sigma weight residual 120.68 117.29 3.39 1.70e+00 3.46e-01 3.97e+00 angle pdb=" C PHE B 142 " pdb=" N ASN B 143 " pdb=" CA ASN B 143 " ideal model delta sigma weight residual 120.68 117.31 3.37 1.70e+00 3.46e-01 3.92e+00 angle pdb=" N THR A 138 " pdb=" CA THR A 138 " pdb=" C THR A 138 " ideal model delta sigma weight residual 111.36 113.48 -2.12 1.09e+00 8.42e-01 3.80e+00 ... (remaining 5567 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.36: 2182 16.36 - 32.72: 128 32.72 - 49.08: 24 49.08 - 65.44: 6 65.44 - 81.80: 2 Dihedral angle restraints: 2342 sinusoidal: 844 harmonic: 1498 Sorted by residual: dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TRP B 95 " pdb=" C TRP B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU B 42 " pdb=" C GLU B 42 " pdb=" N LEU B 43 " pdb=" CA LEU B 43 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 323 0.032 - 0.064: 231 0.064 - 0.096: 64 0.096 - 0.128: 14 0.128 - 0.160: 6 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA THR A 217 " pdb=" N THR A 217 " pdb=" C THR A 217 " pdb=" CB THR A 217 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA THR B 217 " pdb=" N THR B 217 " pdb=" C THR B 217 " pdb=" CB THR B 217 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 635 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 139 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C ILE A 139 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 139 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 139 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C ILE B 139 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 139 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 140 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 270 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C CYS B 270 " 0.039 2.00e-02 2.50e+03 pdb=" O CYS B 270 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS B 271 " -0.013 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.88: 1539 2.88 - 3.45: 4651 3.45 - 4.01: 7541 4.01 - 4.58: 11069 4.58 - 5.14: 15538 Nonbonded interactions: 40338 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OE2 GLU B 79 " model vdw 2.317 3.040 nonbonded pdb=" OE2 GLU A 79 " pdb=" OH TYR B 78 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR A 216 " pdb=" OD1 ASN A 261 " model vdw 2.371 3.040 nonbonded pdb=" OH TYR B 216 " pdb=" OD1 ASN B 261 " model vdw 2.371 3.040 nonbonded pdb=" NH1 ARG A 94 " pdb=" OE1 GLN A 247 " model vdw 2.384 3.120 ... (remaining 40333 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 14 through 295 or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.006 0.040 4110 Z= 0.261 Angle : 0.666 5.041 5572 Z= 0.415 Chirality : 0.045 0.160 638 Planarity : 0.006 0.029 690 Dihedral : 11.556 81.805 1382 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 508 helix: 1.31 (0.23), residues: 416 sheet: None (None), residues: 0 loop : -0.10 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 53 HIS 0.004 0.001 HIS B 77 PHE 0.020 0.002 PHE B 38 TYR 0.019 0.004 TYR B 251 ARG 0.003 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.12492 ( 347) hydrogen bonds : angle 5.03666 ( 1041) covalent geometry : bond 0.00633 ( 4110) covalent geometry : angle 0.66575 ( 5572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.477 Fit side-chains REVERT: A 198 MET cc_start: 0.7665 (ttp) cc_final: 0.7320 (ttt) REVERT: B 198 MET cc_start: 0.7675 (ttp) cc_final: 0.7329 (ttt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1770 time to fit residues: 7.0619 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119579 restraints weight = 4179.966| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.33 r_work: 0.3269 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4110 Z= 0.119 Angle : 0.434 5.502 5572 Z= 0.245 Chirality : 0.034 0.142 638 Planarity : 0.003 0.027 690 Dihedral : 6.593 54.095 592 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 4.25 (0.35), residues: 508 helix: 3.22 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.56 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 53 HIS 0.003 0.001 HIS B 64 PHE 0.007 0.001 PHE B 142 TYR 0.010 0.001 TYR B 251 ARG 0.002 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 347) hydrogen bonds : angle 3.14436 ( 1041) covalent geometry : bond 0.00250 ( 4110) covalent geometry : angle 0.43439 ( 5572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.399 Fit side-chains REVERT: A 80 GLU cc_start: 0.6874 (tt0) cc_final: 0.6573 (mt-10) REVERT: A 198 MET cc_start: 0.6802 (ttp) cc_final: 0.6464 (ttt) REVERT: B 80 GLU cc_start: 0.6860 (tt0) cc_final: 0.6559 (mt-10) REVERT: B 198 MET cc_start: 0.6810 (ttp) cc_final: 0.6474 (ttt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1043 time to fit residues: 3.6948 Evaluate side-chains 20 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 250 HIS B 247 GLN B 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117906 restraints weight = 4178.778| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.34 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4110 Z= 0.132 Angle : 0.424 5.133 5572 Z= 0.236 Chirality : 0.034 0.153 638 Planarity : 0.003 0.026 690 Dihedral : 6.619 56.213 592 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.52 % Allowed : 3.54 % Favored : 94.95 % 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: 4.86 (0.36), residues: 508 helix: 3.60 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 1.05 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 53 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE A 232 TYR 0.010 0.001 TYR A 251 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 347) hydrogen bonds : angle 2.97923 ( 1041) covalent geometry : bond 0.00306 ( 4110) covalent geometry : angle 0.42443 ( 5572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.387 Fit side-chains REVERT: A 80 GLU cc_start: 0.6833 (tt0) cc_final: 0.6572 (mt-10) REVERT: A 198 MET cc_start: 0.6865 (ttp) cc_final: 0.6527 (ttt) REVERT: B 80 GLU cc_start: 0.6831 (tt0) cc_final: 0.6570 (mt-10) REVERT: B 198 MET cc_start: 0.6874 (ttp) cc_final: 0.6536 (ttt) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1023 time to fit residues: 4.1446 Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 250 HIS B 247 GLN B 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116782 restraints weight = 4207.118| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.33 r_work: 0.3230 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4110 Z= 0.141 Angle : 0.421 5.016 5572 Z= 0.235 Chirality : 0.034 0.152 638 Planarity : 0.003 0.027 690 Dihedral : 6.699 56.028 592 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % 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: 4.87 (0.36), residues: 508 helix: 3.64 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.85 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE A 232 TYR 0.009 0.001 TYR A 229 ARG 0.001 0.000 ARG A 94 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 347) hydrogen bonds : angle 2.94233 ( 1041) covalent geometry : bond 0.00332 ( 4110) covalent geometry : angle 0.42067 ( 5572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.404 Fit side-chains REVERT: A 80 GLU cc_start: 0.6846 (tt0) cc_final: 0.6562 (mt-10) REVERT: A 198 MET cc_start: 0.6881 (ttp) cc_final: 0.6552 (ttt) REVERT: B 80 GLU cc_start: 0.6841 (tt0) cc_final: 0.6559 (mt-10) REVERT: B 198 MET cc_start: 0.6898 (ttp) cc_final: 0.6569 (ttt) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.1652 time to fit residues: 5.8018 Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117229 restraints weight = 4304.266| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.36 r_work: 0.3246 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4110 Z= 0.131 Angle : 0.407 4.876 5572 Z= 0.227 Chirality : 0.034 0.149 638 Planarity : 0.003 0.027 690 Dihedral : 6.698 55.978 592 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.02 % Allowed : 4.04 % Favored : 93.94 % 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: 4.92 (0.36), residues: 508 helix: 3.69 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.77 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE B 232 TYR 0.009 0.001 TYR A 229 ARG 0.001 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 347) hydrogen bonds : angle 2.86357 ( 1041) covalent geometry : bond 0.00303 ( 4110) covalent geometry : angle 0.40696 ( 5572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.441 Fit side-chains REVERT: A 80 GLU cc_start: 0.6885 (tt0) cc_final: 0.6583 (mt-10) REVERT: A 198 MET cc_start: 0.6931 (ttp) cc_final: 0.6603 (ttt) REVERT: B 80 GLU cc_start: 0.6870 (tt0) cc_final: 0.6574 (mt-10) REVERT: B 198 MET cc_start: 0.6953 (ttp) cc_final: 0.6622 (ttt) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.1869 time to fit residues: 7.0833 Evaluate side-chains 26 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117674 restraints weight = 4190.088| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.34 r_work: 0.3246 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4110 Z= 0.127 Angle : 0.398 4.894 5572 Z= 0.222 Chirality : 0.033 0.148 638 Planarity : 0.002 0.026 690 Dihedral : 6.700 56.208 592 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.53 % Allowed : 5.05 % Favored : 92.42 % 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: 4.93 (0.36), residues: 508 helix: 3.72 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.67 (0.70), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE A 232 TYR 0.009 0.001 TYR A 229 ARG 0.001 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 347) hydrogen bonds : angle 2.84293 ( 1041) covalent geometry : bond 0.00294 ( 4110) covalent geometry : angle 0.39785 ( 5572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.940 Fit side-chains REVERT: A 80 GLU cc_start: 0.6860 (tt0) cc_final: 0.6537 (mt-10) REVERT: A 198 MET cc_start: 0.6899 (ttp) cc_final: 0.6579 (ttt) REVERT: B 80 GLU cc_start: 0.6841 (tt0) cc_final: 0.6525 (mt-10) REVERT: B 198 MET cc_start: 0.6930 (ttp) cc_final: 0.6607 (ttt) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.2113 time to fit residues: 9.2347 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117789 restraints weight = 4252.029| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.34 r_work: 0.3251 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4110 Z= 0.123 Angle : 0.392 4.850 5572 Z= 0.219 Chirality : 0.033 0.148 638 Planarity : 0.002 0.026 690 Dihedral : 6.698 56.222 592 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.53 % Allowed : 4.55 % Favored : 92.93 % 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: 4.95 (0.36), residues: 508 helix: 3.74 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.59 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 64 PHE 0.008 0.001 PHE A 232 TYR 0.008 0.001 TYR A 229 ARG 0.001 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 347) hydrogen bonds : angle 2.81023 ( 1041) covalent geometry : bond 0.00283 ( 4110) covalent geometry : angle 0.39220 ( 5572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.341 Fit side-chains REVERT: A 80 GLU cc_start: 0.6899 (tt0) cc_final: 0.6566 (mt-10) REVERT: A 198 MET cc_start: 0.6938 (ttp) cc_final: 0.6611 (ttt) REVERT: B 80 GLU cc_start: 0.6882 (tt0) cc_final: 0.6553 (mt-10) REVERT: B 198 MET cc_start: 0.6967 (ttp) cc_final: 0.6639 (ttt) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.2149 time to fit residues: 8.8223 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116248 restraints weight = 4217.125| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.33 r_work: 0.3228 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4110 Z= 0.150 Angle : 0.420 4.901 5572 Z= 0.233 Chirality : 0.034 0.156 638 Planarity : 0.003 0.025 690 Dihedral : 6.779 56.735 592 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.53 % Allowed : 4.55 % Favored : 92.93 % 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: 4.87 (0.36), residues: 508 helix: 3.69 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.54 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE A 232 TYR 0.009 0.001 TYR B 229 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 347) hydrogen bonds : angle 2.90010 ( 1041) covalent geometry : bond 0.00359 ( 4110) covalent geometry : angle 0.41970 ( 5572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.429 Fit side-chains REVERT: A 80 GLU cc_start: 0.6913 (tt0) cc_final: 0.6574 (mt-10) REVERT: B 80 GLU cc_start: 0.6893 (tt0) cc_final: 0.6556 (mt-10) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.2610 time to fit residues: 10.8946 Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119799 restraints weight = 4196.305| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.38 r_work: 0.3277 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4110 Z= 0.099 Angle : 0.368 4.765 5572 Z= 0.207 Chirality : 0.032 0.140 638 Planarity : 0.002 0.025 690 Dihedral : 6.625 56.032 592 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.02 % Allowed : 5.30 % Favored : 92.68 % 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: 5.07 (0.36), residues: 508 helix: 3.82 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.67 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 PHE 0.006 0.001 PHE A 232 TYR 0.007 0.001 TYR A 229 ARG 0.001 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 347) hydrogen bonds : angle 2.73008 ( 1041) covalent geometry : bond 0.00206 ( 4110) covalent geometry : angle 0.36841 ( 5572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.398 Fit side-chains REVERT: A 80 GLU cc_start: 0.6876 (tt0) cc_final: 0.6542 (mt-10) REVERT: B 80 GLU cc_start: 0.6874 (tt0) cc_final: 0.6541 (mt-10) outliers start: 8 outliers final: 8 residues processed: 30 average time/residue: 0.1758 time to fit residues: 7.0948 Evaluate side-chains 31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 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 = 0.3905 r_free = 0.3905 target = 0.159728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118042 restraints weight = 4224.841| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.35 r_work: 0.3257 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4110 Z= 0.122 Angle : 0.392 4.817 5572 Z= 0.219 Chirality : 0.033 0.148 638 Planarity : 0.002 0.024 690 Dihedral : 6.685 56.830 592 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.02 % Allowed : 4.80 % Favored : 93.18 % 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: 5.01 (0.36), residues: 508 helix: 3.79 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.62 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 289 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE B 232 TYR 0.008 0.001 TYR B 229 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 347) hydrogen bonds : angle 2.78173 ( 1041) covalent geometry : bond 0.00281 ( 4110) covalent geometry : angle 0.39222 ( 5572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.480 Fit side-chains REVERT: A 80 GLU cc_start: 0.6922 (tt0) cc_final: 0.6567 (mt-10) REVERT: B 80 GLU cc_start: 0.6901 (tt0) cc_final: 0.6583 (mt-10) outliers start: 8 outliers final: 8 residues processed: 29 average time/residue: 0.1828 time to fit residues: 7.1236 Evaluate side-chains 29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 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 = 0.3899 r_free = 0.3899 target = 0.159082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117466 restraints weight = 4194.094| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.35 r_work: 0.3246 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4110 Z= 0.127 Angle : 0.398 4.818 5572 Z= 0.222 Chirality : 0.033 0.149 638 Planarity : 0.002 0.024 690 Dihedral : 6.713 56.935 592 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.02 % Allowed : 4.80 % Favored : 93.18 % 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: 5.00 (0.36), residues: 508 helix: 3.78 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.61 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 289 HIS 0.002 0.001 HIS A 64 PHE 0.008 0.001 PHE A 232 TYR 0.008 0.001 TYR B 229 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 347) hydrogen bonds : angle 2.79967 ( 1041) covalent geometry : bond 0.00294 ( 4110) covalent geometry : angle 0.39815 ( 5572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.45 seconds wall clock time: 49 minutes 35.48 seconds (2975.48 seconds total)