Starting phenix.real_space_refine on Mon Feb 10 19:49:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.map" model { file = "/net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m65_23689/02_2025/7m65_23689.cif" } resolution = 4.1 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1235 2.51 5 N 370 2.21 5 O 415 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: 2025 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 237 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} 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: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 1.28, per 1000 atoms: 0.63 Number of scatterers: 2025 At special positions: 0 Unit cell: (62.245, 68.575, 45.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 415 8.00 N 370 7.00 C 1235 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 319.4 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.604A pdb=" N THR E 9 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 9 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS A 7 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLN G 10 " --> pdb=" O CYS A 7 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 9 " --> pdb=" O GLN G 10 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR I 9 " --> pdb=" O ALA A 8 " (cutoff:3.500A) 6 hydrogen bonds defined for protein. 18 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: 0.41 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 337 1.31 - 1.44: 613 1.44 - 1.56: 1090 1.56 - 1.68: 0 1.68 - 1.81: 5 Bond restraints: 2045 Sorted by residual: bond pdb=" CG ASN C 35 " pdb=" OD1 ASN C 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.93e+00 bond pdb=" CG ASN E 35 " pdb=" OD1 ASN E 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.78e+00 bond pdb=" CG ASN I 35 " pdb=" OD1 ASN I 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.74e+00 bond pdb=" CG ASN G 35 " pdb=" OD1 ASN G 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.59e+00 bond pdb=" CG ASN A 35 " pdb=" OD1 ASN A 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.55e+00 ... (remaining 2040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 2598 2.33 - 4.67: 132 4.67 - 7.00: 30 7.00 - 9.33: 10 9.33 - 11.66: 5 Bond angle restraints: 2775 Sorted by residual: angle pdb=" N PHE F 15 " pdb=" CA PHE F 15 " pdb=" C PHE F 15 " ideal model delta sigma weight residual 112.41 119.39 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" C PHE J 15 " ideal model delta sigma weight residual 112.41 119.38 -6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" C PHE B 15 " ideal model delta sigma weight residual 112.41 119.37 -6.96 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" C PHE D 15 " ideal model delta sigma weight residual 112.41 119.36 -6.95 1.30e+00 5.92e-01 2.86e+01 angle pdb=" N PHE H 15 " pdb=" CA PHE H 15 " pdb=" C PHE H 15 " ideal model delta sigma weight residual 112.41 119.34 -6.93 1.30e+00 5.92e-01 2.84e+01 ... (remaining 2770 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.26: 870 8.26 - 16.50: 195 16.50 - 24.75: 55 24.75 - 33.00: 35 33.00 - 41.24: 10 Dihedral angle restraints: 1165 sinusoidal: 385 harmonic: 780 Sorted by residual: dihedral pdb=" CA PHE H 15 " pdb=" C PHE H 15 " pdb=" N LEU H 16 " pdb=" CA LEU H 16 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE J 15 " pdb=" C PHE J 15 " pdb=" N LEU J 16 " pdb=" CA LEU J 16 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 15 " pdb=" C PHE D 15 " pdb=" N LEU D 16 " pdb=" CA LEU D 16 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 312 0.132 - 0.264: 23 0.264 - 0.396: 0 0.396 - 0.528: 0 0.528 - 0.660: 5 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE J 26 " pdb=" CA ILE J 26 " pdb=" CG1 ILE J 26 " pdb=" CG2 ILE J 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 337 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE E 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.69e+00 pdb=" CG PHE I 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.68e+00 pdb=" CG PHE A 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 936 2.89 - 3.40: 2346 3.40 - 3.90: 3188 3.90 - 4.40: 3720 4.40 - 4.90: 6916 Nonbonded interactions: 17106 Sorted by model distance: nonbonded pdb=" O LEU J 16 " pdb=" CD2 LEU J 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU D 16 " pdb=" CD2 LEU D 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU B 16 " pdb=" CD2 LEU B 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU F 16 " pdb=" CD2 LEU F 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU H 16 " pdb=" CD2 LEU H 16 " model vdw 2.393 3.460 ... (remaining 17101 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: 0.140 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.050 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 2045 Z= 0.595 Angle : 1.401 11.663 2775 Z= 0.744 Chirality : 0.102 0.660 340 Planarity : 0.004 0.012 360 Dihedral : 12.046 41.242 655 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 33.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.09 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.19), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS H 18 PHE 0.028 0.005 PHE E 15 TYR 0.008 0.002 TYR E 37 ARG 0.001 0.000 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.295 Fit side-chains REVERT: C 15 PHE cc_start: 0.7309 (p90) cc_final: 0.5719 (t80) REVERT: C 28 SER cc_start: 0.8833 (t) cc_final: 0.8519 (p) REVERT: E 28 SER cc_start: 0.8926 (t) cc_final: 0.8483 (p) REVERT: G 28 SER cc_start: 0.9166 (t) cc_final: 0.8770 (p) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1683 time to fit residues: 10.6578 Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.087263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079864 restraints weight = 8972.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.081650 restraints weight = 4744.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.082748 restraints weight = 2922.832| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2045 Z= 0.237 Angle : 0.868 12.195 2775 Z= 0.410 Chirality : 0.045 0.131 340 Planarity : 0.003 0.015 360 Dihedral : 7.741 24.574 275 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % 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: -5.77 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.012 0.003 PHE J 23 TYR 0.005 0.001 TYR G 37 ARG 0.003 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.226 Fit side-chains REVERT: B 22 ASN cc_start: 0.8760 (p0) cc_final: 0.8560 (p0) REVERT: C 28 SER cc_start: 0.8763 (t) cc_final: 0.8558 (p) REVERT: E 27 LEU cc_start: 0.8864 (mp) cc_final: 0.8634 (mp) REVERT: G 28 SER cc_start: 0.9139 (t) cc_final: 0.8721 (p) REVERT: J 22 ASN cc_start: 0.7735 (p0) cc_final: 0.6997 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0855 time to fit residues: 4.3138 Evaluate side-chains 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.090139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.082805 restraints weight = 9576.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.084454 restraints weight = 5195.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.085546 restraints weight = 3219.065| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2045 Z= 0.224 Angle : 0.755 9.544 2775 Z= 0.373 Chirality : 0.044 0.141 340 Planarity : 0.003 0.020 360 Dihedral : 7.176 22.664 275 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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: -5.58 (0.30), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.012 0.002 PHE E 15 TYR 0.004 0.001 TYR E 37 ARG 0.004 0.001 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.177 Fit side-chains REVERT: E 32 VAL cc_start: 0.8210 (p) cc_final: 0.7736 (p) REVERT: G 28 SER cc_start: 0.9243 (t) cc_final: 0.8853 (p) REVERT: J 22 ASN cc_start: 0.7798 (p0) cc_final: 0.7059 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0748 time to fit residues: 3.5537 Evaluate side-chains 26 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 40.0000 chunk 20 optimal weight: 0.0040 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN E 35 ASN I 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.090836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.082605 restraints weight = 8809.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.084387 restraints weight = 4836.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.085596 restraints weight = 3098.864| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2045 Z= 0.165 Angle : 0.729 9.831 2775 Z= 0.345 Chirality : 0.043 0.143 340 Planarity : 0.002 0.013 360 Dihedral : 6.555 21.020 275 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -5.55 (0.30), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 18 PHE 0.010 0.002 PHE G 15 TYR 0.002 0.000 TYR G 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: C 30 THR cc_start: 0.9073 (m) cc_final: 0.8854 (p) REVERT: E 10 GLN cc_start: 0.7901 (mp10) cc_final: 0.7574 (mp10) REVERT: J 22 ASN cc_start: 0.7843 (p0) cc_final: 0.7009 (t0) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0852 time to fit residues: 4.8170 Evaluate side-chains 27 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.092079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.084437 restraints weight = 9693.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.086098 restraints weight = 5272.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087114 restraints weight = 3297.333| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2045 Z= 0.221 Angle : 0.687 8.498 2775 Z= 0.347 Chirality : 0.042 0.136 340 Planarity : 0.003 0.015 360 Dihedral : 6.738 20.173 275 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -5.74 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.012 0.002 PHE H 15 TYR 0.003 0.001 TYR E 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.246 Fit side-chains REVERT: E 10 GLN cc_start: 0.7917 (mp10) cc_final: 0.7633 (mp10) REVERT: J 22 ASN cc_start: 0.7831 (p0) cc_final: 0.6721 (t0) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0679 time to fit residues: 2.9633 Evaluate side-chains 24 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS G 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.089438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.081191 restraints weight = 8865.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.082994 restraints weight = 4919.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.084183 restraints weight = 3142.568| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2045 Z= 0.195 Angle : 0.772 10.364 2775 Z= 0.355 Chirality : 0.044 0.133 340 Planarity : 0.002 0.013 360 Dihedral : 6.656 20.280 275 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -5.71 (0.29), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.011 0.002 PHE D 15 TYR 0.003 0.000 TYR E 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.251 Fit side-chains REVERT: C 30 THR cc_start: 0.9128 (m) cc_final: 0.8920 (p) REVERT: E 10 GLN cc_start: 0.8040 (mp10) cc_final: 0.7677 (mp10) REVERT: E 32 VAL cc_start: 0.8678 (p) cc_final: 0.8465 (p) REVERT: J 22 ASN cc_start: 0.8037 (p0) cc_final: 0.6723 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0652 time to fit residues: 2.9899 Evaluate side-chains 26 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 50.0000 chunk 11 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 overall best weight: 7.3192 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.089138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.081817 restraints weight = 9055.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.083483 restraints weight = 4560.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.084630 restraints weight = 2803.332| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2045 Z= 0.227 Angle : 0.746 9.912 2775 Z= 0.356 Chirality : 0.044 0.138 340 Planarity : 0.003 0.015 360 Dihedral : 6.803 20.238 275 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -5.82 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.013 0.003 PHE E 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.184 Fit side-chains REVERT: E 10 GLN cc_start: 0.8083 (mp10) cc_final: 0.7715 (mp10) REVERT: J 22 ASN cc_start: 0.7844 (p0) cc_final: 0.6246 (t0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0718 time to fit residues: 3.3873 Evaluate side-chains 23 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 40.0000 chunk 16 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.093943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086192 restraints weight = 9300.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.088162 restraints weight = 4874.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.089396 restraints weight = 2964.054| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2045 Z= 0.208 Angle : 0.763 10.126 2775 Z= 0.353 Chirality : 0.044 0.128 340 Planarity : 0.002 0.013 360 Dihedral : 6.699 19.963 275 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -5.71 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.014 0.002 PHE D 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.240 Fit side-chains REVERT: E 10 GLN cc_start: 0.8076 (mp10) cc_final: 0.7736 (mp10) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0612 time to fit residues: 2.8072 Evaluate side-chains 25 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.096429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.088659 restraints weight = 9145.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.090611 restraints weight = 4717.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.091883 restraints weight = 2852.011| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2045 Z= 0.166 Angle : 0.743 11.670 2775 Z= 0.341 Chirality : 0.044 0.152 340 Planarity : 0.002 0.011 360 Dihedral : 6.248 19.903 275 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.57 (0.29), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.012 0.002 PHE D 15 TYR 0.003 0.000 TYR E 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.243 Fit side-chains REVERT: E 10 GLN cc_start: 0.7967 (mp10) cc_final: 0.7660 (mp10) REVERT: J 22 ASN cc_start: 0.7799 (p0) cc_final: 0.6222 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0664 time to fit residues: 3.3485 Evaluate side-chains 24 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.090733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.082935 restraints weight = 8691.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.084727 restraints weight = 4589.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.085880 restraints weight = 2839.139| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2045 Z= 0.219 Angle : 0.798 10.556 2775 Z= 0.366 Chirality : 0.046 0.176 340 Planarity : 0.003 0.012 360 Dihedral : 6.547 20.254 275 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.59 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.014 0.003 PHE G 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.237 Fit side-chains REVERT: E 10 GLN cc_start: 0.8103 (mp10) cc_final: 0.7742 (mp10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0659 time to fit residues: 2.7318 Evaluate side-chains 23 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 50.0000 chunk 16 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.094929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.087206 restraints weight = 9200.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.089126 restraints weight = 4758.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.090324 restraints weight = 2893.471| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2045 Z= 0.213 Angle : 0.762 10.379 2775 Z= 0.355 Chirality : 0.044 0.143 340 Planarity : 0.002 0.012 360 Dihedral : 6.597 18.990 275 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.57 (0.29), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.22), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.013 0.003 PHE C 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 =============================================================================== Job complete usr+sys time: 815.40 seconds wall clock time: 15 minutes 37.61 seconds (937.61 seconds total)