Starting phenix.real_space_refine on Wed Jul 23 06:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.map" model { file = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2025/8z93_39853.cif" } resolution = 4.65 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 309 2.51 5 N 69 2.21 5 O 96 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-5711/modules/chem_data/mon_lib" Total number of atoms: 477 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Restraints were copied for chains: C, B Time building chain proxies: 1.18, per 1000 atoms: 2.47 Number of scatterers: 477 At special positions: 0 Unit cell: (43.46, 40.28, 29.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 96 8.00 N 69 7.00 C 309 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: 0.10 Conformation dependent library (CDL) restraints added in 163.7 milliseconds 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 132 1.33 - 1.45: 105 1.45 - 1.56: 243 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 486 Sorted by residual: bond pdb=" CA MET C 547 " pdb=" CB MET C 547 " ideal model delta sigma weight residual 1.534 1.517 0.017 1.64e-02 3.72e+03 1.05e+00 bond pdb=" CA MET A 547 " pdb=" CB MET A 547 " ideal model delta sigma weight residual 1.534 1.517 0.016 1.64e-02 3.72e+03 1.00e+00 bond pdb=" CA MET B 547 " pdb=" CB MET B 547 " ideal model delta sigma weight residual 1.534 1.518 0.016 1.64e-02 3.72e+03 9.55e-01 bond pdb=" N THR A 537 " pdb=" CA THR A 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.04e-01 bond pdb=" N THR C 537 " pdb=" CA THR C 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.02e-01 ... (remaining 481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 557 1.30 - 2.59: 82 2.59 - 3.88: 15 3.88 - 5.18: 0 5.18 - 6.47: 3 Bond angle restraints: 657 Sorted by residual: angle pdb=" CA TYR A 534 " pdb=" CB TYR A 534 " pdb=" CG TYR A 534 " ideal model delta sigma weight residual 113.90 120.37 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR C 534 " pdb=" CB TYR C 534 " pdb=" CG TYR C 534 " ideal model delta sigma weight residual 113.90 120.36 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR B 534 " pdb=" CB TYR B 534 " pdb=" CG TYR B 534 " ideal model delta sigma weight residual 113.90 120.34 -6.44 1.80e+00 3.09e-01 1.28e+01 angle pdb=" N GLY C 538 " pdb=" CA GLY C 538 " pdb=" C GLY C 538 " ideal model delta sigma weight residual 111.62 115.43 -3.81 1.77e+00 3.19e-01 4.62e+00 angle pdb=" N GLY A 538 " pdb=" CA GLY A 538 " pdb=" C GLY A 538 " ideal model delta sigma weight residual 111.62 115.41 -3.79 1.77e+00 3.19e-01 4.59e+00 ... (remaining 652 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 6.58: 178 6.58 - 13.15: 26 13.15 - 19.72: 39 19.72 - 26.29: 15 26.29 - 32.86: 9 Dihedral angle restraints: 267 sinusoidal: 96 harmonic: 171 Sorted by residual: dihedral pdb=" CA THR B 537 " pdb=" C THR B 537 " pdb=" N GLY B 538 " pdb=" CA GLY B 538 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR C 537 " pdb=" C THR C 537 " pdb=" N GLY C 538 " pdb=" CA GLY C 538 " ideal model delta harmonic sigma weight residual 180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N GLY A 538 " pdb=" CA GLY A 538 " ideal model delta harmonic sigma weight residual 180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 264 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.038: 36 0.038 - 0.075: 18 0.075 - 0.112: 9 0.112 - 0.148: 3 0.148 - 0.185: 3 Chirality restraints: 69 Sorted by residual: chirality pdb=" CA TYR C 534 " pdb=" N TYR C 534 " pdb=" C TYR C 534 " pdb=" CB TYR C 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA TYR B 534 " pdb=" N TYR B 534 " pdb=" C TYR B 534 " pdb=" CB TYR B 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA TYR A 534 " pdb=" N TYR A 534 " pdb=" C TYR A 534 " pdb=" CB TYR A 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 66 not shown) Planarity restraints: 81 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 534 " 0.017 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR B 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 534 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR A 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR C 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " -0.001 2.00e-02 2.50e+03 ... (remaining 78 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 27 2.63 - 3.20: 532 3.20 - 3.76: 702 3.76 - 4.33: 996 4.33 - 4.90: 1471 Nonbonded interactions: 3728 Sorted by model distance: nonbonded pdb=" N TYR B 531 " pdb=" OG1 THR C 532 " model vdw 2.060 3.120 nonbonded pdb=" N GLY B 550 " pdb=" O ILE C 549 " model vdw 2.232 3.120 nonbonded pdb=" O SER A 536 " pdb=" OG1 THR A 537 " model vdw 2.312 3.040 nonbonded pdb=" O SER C 536 " pdb=" OG1 THR C 537 " model vdw 2.313 3.040 nonbonded pdb=" O SER B 536 " pdb=" OG1 THR B 537 " model vdw 2.313 3.040 ... (remaining 3723 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' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 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 0.028 486 Z= 0.307 Angle : 1.053 6.472 657 Z= 0.609 Chirality : 0.065 0.185 69 Planarity : 0.005 0.015 81 Dihedral : 13.343 32.863 165 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 54.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -7.84 (0.52), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.40), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.004 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 486) covalent geometry : angle 1.05252 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0596 time to fit residues: 0.4499 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 overall best weight: 3.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.128854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114886 restraints weight = 542.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.116887 restraints weight = 297.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118709 restraints weight = 221.738| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5270 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 486 Z= 0.346 Angle : 1.032 5.126 657 Z= 0.586 Chirality : 0.082 0.195 69 Planarity : 0.008 0.018 81 Dihedral : 11.181 27.786 69 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 45.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % 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: -8.37 (0.44), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.37 (0.34), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.006 TYR C 544 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 486) covalent geometry : angle 1.03234 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0562 time to fit residues: 0.3114 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.135586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.115893 restraints weight = 461.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.119056 restraints weight = 274.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.120512 restraints weight = 193.867| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 486 Z= 0.294 Angle : 1.017 5.788 657 Z= 0.566 Chirality : 0.079 0.159 69 Planarity : 0.006 0.013 81 Dihedral : 10.543 27.381 69 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 35.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % Rotamer: Outliers : 6.25 % Allowed : 6.25 % Favored : 87.50 % 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: -8.27 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.30 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.003 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 486) covalent geometry : angle 1.01715 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.019 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.0757 time to fit residues: 0.4200 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.153455 restraints weight = 356.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156591 restraints weight = 211.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.158597 restraints weight = 141.122| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5145 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 486 Z= 0.321 Angle : 1.000 6.396 657 Z= 0.575 Chirality : 0.082 0.198 69 Planarity : 0.007 0.019 81 Dihedral : 9.693 20.911 69 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 43.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.44 % Favored : 55.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -8.41 (0.50), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.40 (0.38), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.004 TYR A 544 Details of bonding type rmsd covalent geometry : bond 0.00709 ( 486) covalent geometry : angle 1.00038 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0663 time to fit residues: 0.4377 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.206634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.153548 restraints weight = 280.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.155735 restraints weight = 179.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.156962 restraints weight = 132.651| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.8429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 486 Z= 0.332 Angle : 1.030 5.538 657 Z= 0.578 Chirality : 0.074 0.151 69 Planarity : 0.006 0.013 81 Dihedral : 11.520 26.465 69 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -8.45 (0.41), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.31), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.004 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 486) covalent geometry : angle 1.02979 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0534 time to fit residues: 0.3580 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.207314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.178673 restraints weight = 316.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182103 restraints weight = 194.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184599 restraints weight = 141.019| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5179 moved from start: 0.9164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 486 Z= 0.209 Angle : 0.862 4.918 657 Z= 0.492 Chirality : 0.069 0.142 69 Planarity : 0.005 0.010 81 Dihedral : 9.367 24.068 69 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 39.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.80 (0.54), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.94 (0.41), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.004 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 486) covalent geometry : angle 0.86189 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0627 time to fit residues: 0.4159 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.172196 restraints weight = 292.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175707 restraints weight = 186.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.177571 restraints weight = 136.516| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 1.0337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 486 Z= 0.171 Angle : 0.826 4.853 657 Z= 0.478 Chirality : 0.070 0.138 69 Planarity : 0.004 0.012 81 Dihedral : 8.902 19.714 69 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 38.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.44 % Favored : 55.56 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -7.74 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.89 (0.38), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 486) covalent geometry : angle 0.82551 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0614 time to fit residues: 0.4091 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 overall best weight: 3.0283 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.222820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158903 restraints weight = 283.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.160422 restraints weight = 223.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.162061 restraints weight = 192.321| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5003 moved from start: 0.9859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 486 Z= 0.259 Angle : 0.920 5.502 657 Z= 0.517 Chirality : 0.070 0.149 69 Planarity : 0.006 0.018 81 Dihedral : 10.102 21.975 69 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.44 % Favored : 55.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.78 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.92 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.005 TYR B 544 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 486) covalent geometry : angle 0.91998 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 Fit side-chains REVERT: A 534 TYR cc_start: 0.5539 (p90) cc_final: 0.4603 (m-10) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0612 time to fit residues: 0.4071 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.209709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.173019 restraints weight = 298.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.176004 restraints weight = 220.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.177812 restraints weight = 170.587| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 0.9746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 486 Z= 0.314 Angle : 1.000 5.303 657 Z= 0.553 Chirality : 0.072 0.155 69 Planarity : 0.006 0.017 81 Dihedral : 11.288 25.254 69 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.80 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.94 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.042 0.005 TYR B 544 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 486) covalent geometry : angle 0.99959 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0595 time to fit residues: 0.2731 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.153734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137739 restraints weight = 496.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137738 restraints weight = 464.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137738 restraints weight = 464.628| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.9578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 486 Z= 0.331 Angle : 0.993 5.164 657 Z= 0.550 Chirality : 0.073 0.149 69 Planarity : 0.006 0.017 81 Dihedral : 11.782 24.779 69 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 37.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.59 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.78 (0.38), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.005 TYR B 544 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 486) covalent geometry : angle 0.99285 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0581 time to fit residues: 0.2690 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 5.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.154788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.138669 restraints weight = 514.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.138738 restraints weight = 451.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.138738 restraints weight = 443.543| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 486 Z= 0.401 Angle : 1.114 5.083 657 Z= 0.601 Chirality : 0.078 0.156 69 Planarity : 0.007 0.016 81 Dihedral : 12.004 25.317 69 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 51.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.20 (0.60), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.48 (0.46), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.038 0.005 TYR B 544 Details of bonding type rmsd covalent geometry : bond 0.00904 ( 486) covalent geometry : angle 1.11401 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 482.46 seconds wall clock time: 10 minutes 24.95 seconds (624.95 seconds total)