Starting phenix.real_space_refine on Mon Feb 10 19:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.map" model { file = "/net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vqq_32092/02_2025/7vqq_32092.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 1158 2.51 5 N 327 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1968 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "B" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "C" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Time building chain proxies: 2.19, per 1000 atoms: 1.11 Number of scatterers: 1968 At special positions: 0 Unit cell: (80.3, 83.6, 30.8, 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 483 8.00 N 327 7.00 C 1158 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: 0.95 Conformation dependent library (CDL) restraints added in 508.3 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 444 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 6.676A pdb=" N SER A 56 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 56 " --> pdb=" O SER C 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.353A pdb=" N ASN B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.503A pdb=" N SER C 70 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.734A pdb=" N GLN A 73 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN B 73 " --> pdb=" O GLY C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.345A pdb=" N TYR A 81 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 81 " --> pdb=" O GLY C 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 93 through 96 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: 0.39 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 333 1.28 - 1.35: 322 1.35 - 1.41: 337 1.41 - 1.47: 346 1.47 - 1.54: 681 Bond restraints: 2019 Sorted by residual: bond pdb=" C ALA A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 5.02e+00 bond pdb=" C TYR B 91 " pdb=" N GLY B 92 " ideal model delta sigma weight residual 1.330 1.308 0.021 1.31e-02 5.83e+03 2.64e+00 bond pdb=" CA GLY B 92 " pdb=" C GLY B 92 " ideal model delta sigma weight residual 1.517 1.496 0.021 1.43e-02 4.89e+03 2.24e+00 bond pdb=" CA GLN C 118 " pdb=" CB GLN C 118 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.69e-02 3.50e+03 2.04e+00 bond pdb=" N GLY A 65 " pdb=" CA GLY A 65 " ideal model delta sigma weight residual 1.460 1.442 0.018 1.26e-02 6.30e+03 2.03e+00 ... (remaining 2014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2352 1.11 - 2.22: 306 2.22 - 3.33: 57 3.33 - 4.44: 14 4.44 - 5.55: 4 Bond angle restraints: 2733 Sorted by residual: angle pdb=" CA TYR C 38 " pdb=" CB TYR C 38 " pdb=" CG TYR C 38 " ideal model delta sigma weight residual 113.90 108.92 4.98 1.80e+00 3.09e-01 7.64e+00 angle pdb=" CA GLY C 82 " pdb=" C GLY C 82 " pdb=" N SER C 83 " ideal model delta sigma weight residual 115.49 118.02 -2.53 1.03e+00 9.43e-01 6.01e+00 angle pdb=" CA GLY C 76 " pdb=" C GLY C 76 " pdb=" N SER C 77 " ideal model delta sigma weight residual 115.09 118.18 -3.09 1.29e+00 6.01e-01 5.73e+00 angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 109.60 4.30 1.80e+00 3.09e-01 5.72e+00 angle pdb=" N GLY A 59 " pdb=" CA GLY A 59 " pdb=" C GLY A 59 " ideal model delta sigma weight residual 113.18 118.73 -5.55 2.37e+00 1.78e-01 5.49e+00 ... (remaining 2728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.17: 1007 13.17 - 26.34: 117 26.34 - 39.51: 19 39.51 - 52.68: 4 52.68 - 65.85: 2 Dihedral angle restraints: 1149 sinusoidal: 390 harmonic: 759 Sorted by residual: dihedral pdb=" CA TYR A 91 " pdb=" C TYR A 91 " pdb=" N GLY A 92 " pdb=" CA GLY A 92 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLY C 92 " pdb=" CA GLY C 92 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 58 " pdb=" C TYR B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 143 0.029 - 0.057: 52 0.057 - 0.086: 28 0.086 - 0.115: 13 0.115 - 0.143: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA TYR B 41 " pdb=" N TYR B 41 " pdb=" C TYR B 41 " pdb=" CB TYR B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA TYR C 41 " pdb=" N TYR C 41 " pdb=" C TYR C 41 " pdb=" CB TYR C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA TYR A 41 " pdb=" N TYR A 41 " pdb=" C TYR A 41 " pdb=" CB TYR A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 240 not shown) Planarity restraints: 381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 71 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 72 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 71 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 72 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 104 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.020 5.00e-02 4.00e+02 ... (remaining 378 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 504 2.77 - 3.30: 1610 3.30 - 3.83: 2713 3.83 - 4.37: 3259 4.37 - 4.90: 6117 Nonbonded interactions: 14203 Sorted by model distance: nonbonded pdb=" O SER A 39 " pdb=" OG SER A 39 " model vdw 2.233 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 71 " pdb=" OG1 THR A 71 " model vdw 2.396 3.040 nonbonded pdb=" O TYR B 41 " pdb=" OG SER B 44 " model vdw 2.410 3.040 nonbonded pdb=" O THR C 71 " pdb=" OG1 THR C 71 " model vdw 2.417 3.040 ... (remaining 14198 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 92 or resid 94 through 124)) selection = (chain 'B' and (resid 34 through 92 or resid 94 through 124)) selection = (chain 'C' and (resid 34 through 92 or resid 94 through 124)) } 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=0.00 max=1.00 mean=0.99 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.160 Find NCS groups from input model: 0.090 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.009 0.044 2019 Z= 0.569 Angle : 0.847 5.552 2733 Z= 0.486 Chirality : 0.047 0.143 243 Planarity : 0.006 0.044 381 Dihedral : 11.510 65.851 705 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: -6.09 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1773 time to fit residues: 3.9765 Evaluate side-chains 15 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 93 GLN B A 103 GLN B 88 GLN B 93 GLN B B 103 GLN C 88 GLN C 94 GLN C 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080716 restraints weight = 9464.967| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.15 r_work: 0.3085 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2019 Z= 0.115 Angle : 0.538 4.016 2733 Z= 0.289 Chirality : 0.037 0.126 243 Planarity : 0.004 0.026 381 Dihedral : 4.052 15.164 315 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.37 % Allowed : 5.48 % Favored : 93.15 % 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: -5.46 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.190 Fit side-chains REVERT: B 103 GLN cc_start: 0.7814 (mt0) cc_final: 0.7575 (mt0) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.2967 time to fit residues: 5.9525 Evaluate side-chains 17 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 overall best weight: 3.5444 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.099740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076687 restraints weight = 8377.624| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.81 r_work: 0.3013 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2019 Z= 0.300 Angle : 0.658 4.968 2733 Z= 0.358 Chirality : 0.040 0.142 243 Planarity : 0.004 0.030 381 Dihedral : 4.504 15.606 315 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.74 % Allowed : 6.85 % Favored : 90.41 % 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: -5.42 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.163 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.2032 time to fit residues: 4.0392 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.099095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075230 restraints weight = 12722.688| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.44 r_work: 0.2970 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2019 Z= 0.346 Angle : 0.700 5.665 2733 Z= 0.381 Chirality : 0.043 0.174 243 Planarity : 0.004 0.033 381 Dihedral : 4.645 15.575 315 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.74 % Allowed : 8.22 % Favored : 89.04 % 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: -5.34 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.217 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 17 average time/residue: 0.2003 time to fit residues: 4.0041 Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.100044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076859 restraints weight = 8979.480| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.95 r_work: 0.3013 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2019 Z= 0.251 Angle : 0.634 5.108 2733 Z= 0.343 Chirality : 0.040 0.157 243 Planarity : 0.004 0.029 381 Dihedral : 4.413 15.282 315 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.74 % Allowed : 9.13 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.219 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 16 average time/residue: 0.2187 time to fit residues: 4.1261 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.102588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078619 restraints weight = 12947.140| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.55 r_work: 0.3035 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2019 Z= 0.141 Angle : 0.548 4.178 2733 Z= 0.293 Chirality : 0.037 0.124 243 Planarity : 0.003 0.023 381 Dihedral : 3.945 14.819 315 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.28 % Allowed : 9.59 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.199 Fit side-chains REVERT: A 90 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8351 (p) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.2065 time to fit residues: 3.8727 Evaluate side-chains 18 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.099230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075911 restraints weight = 9708.202| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.05 r_work: 0.2992 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2019 Z= 0.329 Angle : 0.674 5.397 2733 Z= 0.366 Chirality : 0.041 0.160 243 Planarity : 0.004 0.027 381 Dihedral : 4.451 14.747 315 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.20 % Allowed : 9.13 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.208 Fit side-chains REVERT: A 90 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8212 (p) outliers start: 7 outliers final: 5 residues processed: 16 average time/residue: 0.2040 time to fit residues: 3.8455 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077444 restraints weight = 10200.366| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.20 r_work: 0.3010 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2019 Z= 0.237 Angle : 0.620 4.985 2733 Z= 0.334 Chirality : 0.040 0.156 243 Planarity : 0.003 0.024 381 Dihedral : 4.292 14.823 315 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 9.59 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.216 Fit side-chains REVERT: A 90 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (p) outliers start: 6 outliers final: 5 residues processed: 16 average time/residue: 0.1969 time to fit residues: 3.7249 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.077203 restraints weight = 11765.773| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 4.31 r_work: 0.3007 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2019 Z= 0.207 Angle : 0.604 5.030 2733 Z= 0.324 Chirality : 0.039 0.145 243 Planarity : 0.003 0.024 381 Dihedral : 4.177 14.497 315 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.74 % Allowed : 10.05 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.216 Fit side-chains REVERT: A 90 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8250 (p) outliers start: 6 outliers final: 5 residues processed: 16 average time/residue: 0.2020 time to fit residues: 3.7954 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075159 restraints weight = 12854.356| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.41 r_work: 0.2969 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2019 Z= 0.345 Angle : 0.700 5.758 2733 Z= 0.379 Chirality : 0.042 0.171 243 Planarity : 0.004 0.027 381 Dihedral : 4.514 14.645 315 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.20 % Allowed : 9.59 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.204 Fit side-chains REVERT: A 90 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8261 (p) outliers start: 7 outliers final: 5 residues processed: 16 average time/residue: 0.2039 time to fit residues: 3.8204 Evaluate side-chains 19 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077919 restraints weight = 10161.779| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.18 r_work: 0.3020 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2019 Z= 0.191 Angle : 0.598 5.399 2733 Z= 0.320 Chirality : 0.039 0.147 243 Planarity : 0.003 0.023 381 Dihedral : 4.177 14.553 315 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.28 % Allowed : 10.50 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.91 seconds wall clock time: 26 minutes 13.01 seconds (1573.01 seconds total)