Starting phenix.real_space_refine on Wed Mar 5 14:23:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.map" model { file = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m61_23686/03_2025/7m61_23686.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1030 2.51 5 N 305 2.21 5 O 355 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-5624/modules/chem_data/mon_lib" Total number of atoms: 1690 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 152 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.89, per 1000 atoms: 0.53 Number of scatterers: 1690 At special positions: 0 Unit cell: (59.08, 51.695, 48.53, 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 355 8.00 N 305 7.00 C 1030 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 208.0 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 15 removed outlier: 7.243A pdb=" N ASN A 14 " --> pdb=" O PHE G 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.100A pdb=" N ASN A 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 23 through 25 removed outlier: 6.755A pdb=" N ALA F 25 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA H 25 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE B 23 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA J 25 " --> pdb=" O GLY B 24 " (cutoff:3.500A) 9 hydrogen bonds defined for protein. 27 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: 0.31 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 275 1.29 - 1.35: 293 1.35 - 1.42: 232 1.42 - 1.48: 250 1.48 - 1.55: 655 Bond restraints: 1705 Sorted by residual: bond pdb=" CB ILE E 26 " pdb=" CG1 ILE E 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CB ILE I 26 " pdb=" CG1 ILE I 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE C 26 " pdb=" CG1 ILE C 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CB ILE G 26 " pdb=" CG1 ILE G 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" CB ILE A 26 " pdb=" CG1 ILE A 26 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 1700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 2236 1.84 - 3.69: 59 3.69 - 5.53: 0 5.53 - 7.38: 5 7.38 - 9.22: 15 Bond angle restraints: 2315 Sorted by residual: angle pdb=" CG1 ILE A 26 " pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 110.70 101.48 9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" CG1 ILE I 26 " pdb=" CB ILE I 26 " pdb=" CG2 ILE I 26 " ideal model delta sigma weight residual 110.70 101.49 9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" CG1 ILE G 26 " pdb=" CB ILE G 26 " pdb=" CG2 ILE G 26 " ideal model delta sigma weight residual 110.70 101.51 9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" CG1 ILE E 26 " pdb=" CB ILE E 26 " pdb=" CG2 ILE E 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" CG1 ILE C 26 " pdb=" CB ILE C 26 " pdb=" CG2 ILE C 26 " ideal model delta sigma weight residual 110.70 101.52 9.18 3.00e+00 1.11e-01 9.35e+00 ... (remaining 2310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.63: 780 8.63 - 17.25: 90 17.25 - 25.87: 40 25.87 - 34.50: 20 34.50 - 43.12: 20 Dihedral angle restraints: 950 sinusoidal: 300 harmonic: 650 Sorted by residual: dihedral pdb=" CA PHE I 15 " pdb=" C PHE I 15 " pdb=" N LEU I 16 " pdb=" CA LEU I 16 " ideal model delta harmonic sigma weight residual 180.00 167.01 12.99 0 5.00e+00 4.00e-02 6.75e+00 dihedral pdb=" CA PHE G 15 " pdb=" C PHE G 15 " pdb=" N LEU G 16 " pdb=" CA LEU G 16 " ideal model delta harmonic sigma weight residual 180.00 167.04 12.96 0 5.00e+00 4.00e-02 6.72e+00 dihedral pdb=" CA PHE A 15 " pdb=" C PHE A 15 " pdb=" N LEU A 16 " pdb=" CA LEU A 16 " ideal model delta harmonic sigma weight residual 180.00 167.07 12.93 0 5.00e+00 4.00e-02 6.69e+00 ... (remaining 947 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.061: 200 0.061 - 0.121: 51 0.121 - 0.181: 9 0.181 - 0.241: 10 0.241 - 0.301: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CG LEU B 27 " pdb=" CB LEU B 27 " pdb=" CD1 LEU B 27 " pdb=" CD2 LEU B 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU D 27 " pdb=" CB LEU D 27 " pdb=" CD1 LEU D 27 " pdb=" CD2 LEU D 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU F 27 " pdb=" CB LEU F 27 " pdb=" CD1 LEU F 27 " pdb=" CD2 LEU F 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 272 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR J 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR J 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR J 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR J 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR J 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR F 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR F 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR F 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " -0.015 2.00e-02 2.50e+03 1.72e-02 5.91e+00 pdb=" CG TYR B 37 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 291 2.75 - 3.29: 1811 3.29 - 3.83: 2864 3.83 - 4.36: 3257 4.36 - 4.90: 6142 Nonbonded interactions: 14365 Sorted by model distance: nonbonded pdb=" O SER E 34 " pdb=" OG SER G 34 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 34 " pdb=" OG SER I 34 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 34 " pdb=" O SER G 34 " model vdw 2.218 3.040 nonbonded pdb=" O SER C 34 " pdb=" OG SER E 34 " model vdw 2.218 3.040 nonbonded pdb=" ND2 ASN G 22 " pdb=" O GLY G 24 " model vdw 2.433 3.120 ... (remaining 14360 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.005 0.037 1705 Z= 0.301 Angle : 1.018 9.221 2315 Z= 0.508 Chirality : 0.076 0.301 275 Planarity : 0.003 0.017 300 Dihedral : 12.788 43.118 530 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -4.63 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.005 0.001 PHE H 23 TYR 0.040 0.006 TYR J 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0664 time to fit residues: 3.5389 Evaluate side-chains 21 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.100865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.088108 restraints weight = 4809.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090360 restraints weight = 2463.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.091923 restraints weight = 1585.409| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1705 Z= 0.237 Angle : 0.731 7.871 2315 Z= 0.361 Chirality : 0.049 0.166 275 Planarity : 0.003 0.010 300 Dihedral : 5.047 14.067 230 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.05 % Allowed : 13.85 % Favored : 84.10 % 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: -4.99 (0.30), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.23), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 18 PHE 0.011 0.002 PHE F 23 TYR 0.024 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.338 Fit side-chains REVERT: B 29 SER cc_start: 0.8981 (t) cc_final: 0.8745 (p) REVERT: E 15 PHE cc_start: 0.8320 (m-10) cc_final: 0.8067 (m-80) REVERT: H 23 PHE cc_start: 0.8400 (m-80) cc_final: 0.7973 (m-80) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.0682 time to fit residues: 3.5021 Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain F residue 37 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 40.0000 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.095771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082936 restraints weight = 5394.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.084974 restraints weight = 2879.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.086398 restraints weight = 1931.703| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1705 Z= 0.263 Angle : 0.728 7.947 2315 Z= 0.360 Chirality : 0.047 0.183 275 Planarity : 0.003 0.010 300 Dihedral : 5.374 15.604 230 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 6.15 % Allowed : 14.36 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.011 0.002 PHE F 23 TYR 0.024 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.193 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 30 average time/residue: 0.0552 time to fit residues: 2.3098 Evaluate side-chains 23 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.096749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.083821 restraints weight = 5239.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085613 restraints weight = 3023.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086626 restraints weight = 2175.292| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1705 Z= 0.255 Angle : 0.660 6.898 2315 Z= 0.339 Chirality : 0.045 0.161 275 Planarity : 0.002 0.009 300 Dihedral : 5.324 14.322 230 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 6.15 % Allowed : 17.44 % Favored : 76.41 % 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: -4.99 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.011 0.002 PHE F 23 TYR 0.020 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 26 average time/residue: 0.0670 time to fit residues: 2.4228 Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 14 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.114044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091500 restraints weight = 5692.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093517 restraints weight = 3356.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.094948 restraints weight = 2388.741| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 1705 Z= 0.334 Angle : 0.710 8.186 2315 Z= 0.369 Chirality : 0.046 0.140 275 Planarity : 0.003 0.010 300 Dihedral : 5.785 16.960 230 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 5.64 % Allowed : 23.08 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.013 0.002 PHE F 23 TYR 0.023 0.003 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8882 (p0) outliers start: 11 outliers final: 9 residues processed: 25 average time/residue: 0.0665 time to fit residues: 2.3188 Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 overall best weight: 6.5190 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.117858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.095358 restraints weight = 5760.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097364 restraints weight = 3405.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.098808 restraints weight = 2427.653| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1705 Z= 0.257 Angle : 0.673 7.998 2315 Z= 0.339 Chirality : 0.043 0.130 275 Planarity : 0.002 0.008 300 Dihedral : 5.361 14.892 230 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 5.64 % Allowed : 23.59 % Favored : 70.77 % 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 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.014 0.002 PHE F 23 TYR 0.018 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8838 (p0) outliers start: 11 outliers final: 9 residues processed: 27 average time/residue: 0.0658 time to fit residues: 2.4628 Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.106127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.093367 restraints weight = 5125.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.095354 restraints weight = 2936.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.096782 restraints weight = 2056.863| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1705 Z= 0.289 Angle : 0.692 8.280 2315 Z= 0.352 Chirality : 0.045 0.135 275 Planarity : 0.002 0.008 300 Dihedral : 5.587 15.757 230 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.19 % Favored : 83.81 % Rotamer: Outliers : 8.72 % Allowed : 21.03 % Favored : 70.26 % 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: -4.96 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.015 0.002 PHE F 23 TYR 0.019 0.002 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8849 (p0) outliers start: 17 outliers final: 12 residues processed: 30 average time/residue: 0.0640 time to fit residues: 2.6171 Evaluate side-chains 28 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 15 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 9 optimal weight: 0.0270 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 3.9644 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.104686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.091463 restraints weight = 5039.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.093385 restraints weight = 2937.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.094650 restraints weight = 2108.690| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1705 Z= 0.186 Angle : 0.664 8.941 2315 Z= 0.324 Chirality : 0.045 0.249 275 Planarity : 0.002 0.008 300 Dihedral : 4.910 14.590 230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 7.18 % Allowed : 22.56 % Favored : 70.26 % 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: -4.99 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.012 0.001 PHE E 15 TYR 0.013 0.001 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 20 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 32 average time/residue: 0.0637 time to fit residues: 2.7975 Evaluate side-chains 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 PHE Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.111084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.097781 restraints weight = 5010.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.099963 restraints weight = 2889.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.101564 restraints weight = 2011.277| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1705 Z= 0.180 Angle : 0.660 8.507 2315 Z= 0.316 Chirality : 0.045 0.232 275 Planarity : 0.002 0.007 300 Dihedral : 4.820 14.508 230 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 5.13 % Allowed : 24.62 % Favored : 70.26 % 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: -4.96 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 18 PHE 0.012 0.001 PHE E 15 TYR 0.013 0.001 TYR H 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 26 average time/residue: 0.0616 time to fit residues: 2.2373 Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 4 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.111160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.097992 restraints weight = 5169.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.100227 restraints weight = 2875.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.101455 restraints weight = 1990.364| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1705 Z= 0.204 Angle : 0.695 8.472 2315 Z= 0.331 Chirality : 0.048 0.226 275 Planarity : 0.002 0.009 300 Dihedral : 4.933 14.234 230 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 4.10 % Allowed : 24.10 % Favored : 71.79 % 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 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.013 0.001 PHE F 23 TYR 0.014 0.001 TYR H 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 25 average time/residue: 0.0656 time to fit residues: 2.2989 Evaluate side-chains 22 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 23 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain J residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.0370 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 5.6066 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.103733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.090407 restraints weight = 5173.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092235 restraints weight = 3035.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093512 restraints weight = 2213.051| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1705 Z= 0.229 Angle : 0.712 8.704 2315 Z= 0.340 Chirality : 0.049 0.234 275 Planarity : 0.002 0.008 300 Dihedral : 5.134 13.984 230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 5.13 % Allowed : 23.59 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.015 0.002 PHE F 23 TYR 0.016 0.002 TYR H 37 =============================================================================== Job complete usr+sys time: 808.62 seconds wall clock time: 14 minutes 43.71 seconds (883.71 seconds total)