Starting phenix.real_space_refine on Mon Feb 10 19:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m61_23686/02_2025/7m61_23686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m61_23686/02_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_23686/02_2025/7m61_23686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m61_23686/02_2025/7m61_23686.map" model { file = "/net/cci-nas-00/data/ceres_data/7m61_23686/02_2025/7m61_23686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m61_23686/02_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-5592/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: 0.85, per 1000 atoms: 0.50 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: 0.67 Conformation dependent library (CDL) restraints added in 204.4 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: 0.19 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- 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 : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0620 time to fit residues: 3.3115 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 : 0.197 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.088110 restraints weight = 4809.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.090375 restraints weight = 2464.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.091944 restraints weight = 1582.515| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- 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 14.066 230 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 : 0.205 Fit side-chains REVERT: B 29 SER cc_start: 0.8978 (t) cc_final: 0.8743 (p) REVERT: E 15 PHE cc_start: 0.8319 (m-10) cc_final: 0.8066 (m-80) REVERT: H 23 PHE cc_start: 0.8401 (m-80) cc_final: 0.7975 (m-80) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.0700 time to fit residues: 3.5827 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 : 0.198 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 7 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.098133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.085170 restraints weight = 5455.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087145 restraints weight = 3087.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.088500 restraints weight = 2162.023| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3543 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= 0.239 Angle : 0.709 7.898 2315 Z= 0.349 Chirality : 0.046 0.182 275 Planarity : 0.002 0.009 300 Dihedral : 5.197 15.141 230 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 5.64 % Allowed : 14.36 % Favored : 80.00 % 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: -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 C 18 PHE 0.010 0.002 PHE F 23 TYR 0.022 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 35 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.206 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 29 average time/residue: 0.0641 time to fit residues: 2.5720 Evaluate side-chains 24 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 15 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 17 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 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: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.096263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083120 restraints weight = 5280.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.085034 restraints weight = 2957.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086170 restraints weight = 2083.479| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4167 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= 0.273 Angle : 0.670 7.058 2315 Z= 0.342 Chirality : 0.046 0.169 275 Planarity : 0.002 0.009 300 Dihedral : 5.447 14.034 230 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 6.67 % Allowed : 16.41 % Favored : 76.92 % 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 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (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 32 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 28 average time/residue: 0.0628 time to fit residues: 2.4464 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 : 0.200 ------------------------------------------------------------------------------- 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: 20.0000 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 0.0970 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.114867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.093651 restraints weight = 5655.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.095610 restraints weight = 3375.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096718 restraints weight = 2425.600| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4585 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= 0.248 Angle : 0.645 7.769 2315 Z= 0.331 Chirality : 0.044 0.133 275 Planarity : 0.002 0.008 300 Dihedral : 5.360 14.816 230 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 6.67 % Allowed : 22.05 % 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: -4.95 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 18 PHE 0.011 0.002 PHE F 23 TYR 0.019 0.002 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 30 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8884 (p0) REVERT: J 37 TYR cc_start: 0.7767 (m-10) cc_final: 0.4817 (p90) outliers start: 13 outliers final: 8 residues processed: 26 average time/residue: 0.0585 time to fit residues: 2.1854 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 : 0.196 ------------------------------------------------------------------------------- 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 E residue 17 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.107722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094617 restraints weight = 5133.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096690 restraints weight = 2980.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098203 restraints weight = 2094.689| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1705 Z= 0.229 Angle : 0.631 8.709 2315 Z= 0.321 Chirality : 0.043 0.127 275 Planarity : 0.002 0.008 300 Dihedral : 5.175 14.506 230 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 6.67 % Allowed : 23.08 % 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 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.24), 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 0.020 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 31 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (p0) outliers start: 13 outliers final: 9 residues processed: 27 average time/residue: 0.0615 time to fit residues: 2.3200 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 : 0.174 ------------------------------------------------------------------------------- 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 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 I residue 31 ASN 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: 20.0000 chunk 11 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 40.0000 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.103504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.090270 restraints weight = 5057.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092076 restraints weight = 2967.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093454 restraints weight = 2149.961| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5025 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= 0.206 Angle : 0.636 8.275 2315 Z= 0.313 Chirality : 0.043 0.126 275 Planarity : 0.002 0.008 300 Dihedral : 4.969 14.017 230 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 7.69 % Allowed : 22.05 % 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: -4.98 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 18 PHE 0.011 0.001 PHE F 23 TYR 0.016 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: 15 poor density : 18 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8917 (p0) outliers start: 15 outliers final: 11 residues processed: 29 average time/residue: 0.0633 time to fit residues: 2.5507 Evaluate side-chains 29 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 4 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.0060 chunk 16 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 2.5600 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.107430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093966 restraints weight = 4954.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.095962 restraints weight = 2898.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097326 restraints weight = 2071.611| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1705 Z= 0.148 Angle : 0.624 8.837 2315 Z= 0.297 Chirality : 0.043 0.244 275 Planarity : 0.002 0.007 300 Dihedral : 4.426 13.636 230 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.59 % Allowed : 25.64 % 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: -4.95 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.23), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 18 PHE 0.011 0.001 PHE E 15 TYR 0.011 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 31 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 15 PHE cc_start: 0.8049 (m-80) cc_final: 0.7797 (m-10) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0614 time to fit residues: 2.4242 Evaluate side-chains 23 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 37 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.108331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095670 restraints weight = 5189.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097718 restraints weight = 2904.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.099195 restraints weight = 2025.421| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5290 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= 0.274 Angle : 0.707 8.983 2315 Z= 0.347 Chirality : 0.049 0.235 275 Planarity : 0.002 0.008 300 Dihedral : 5.349 15.239 230 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 5.13 % Allowed : 24.10 % 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: -4.93 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (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 0.018 0.002 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 27 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 25 average time/residue: 0.0669 time to fit residues: 2.3232 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 : 0.201 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.094921 restraints weight = 5326.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.096923 restraints weight = 3037.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.098395 restraints weight = 2132.213| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5431 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= 0.278 Angle : 0.720 8.907 2315 Z= 0.356 Chirality : 0.049 0.234 275 Planarity : 0.002 0.008 300 Dihedral : 5.511 15.648 230 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 4.10 % Allowed : 25.13 % 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: -4.91 (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 0.014 0.002 PHE E 15 TYR 0.019 0.002 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 22 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.180 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: 20 average time/residue: 0.0612 time to fit residues: 1.7568 Evaluate side-chains 21 residues out of total 195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.111028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098051 restraints weight = 5064.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.100287 restraints weight = 2914.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.101474 restraints weight = 2025.324| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5484 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= 0.197 Angle : 0.670 8.589 2315 Z= 0.324 Chirality : 0.047 0.225 275 Planarity : 0.002 0.009 300 Dihedral : 4.893 13.945 230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 4.10 % Allowed : 25.13 % 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: -4.93 (0.32), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 18 PHE 0.013 0.001 PHE E 15 TYR 0.013 0.001 TYR H 37 =============================================================================== Job complete usr+sys time: 742.53 seconds wall clock time: 14 minutes 1.80 seconds (841.80 seconds total)