Starting phenix.real_space_refine on Wed Mar 5 14:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m65_23689/03_2025/7m65_23689.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m65_23689/03_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_23689/03_2025/7m65_23689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2025/7m65_23689.map" model { file = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_2025/7m65_23689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m65_23689/03_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-5624/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: 1.31, per 1000 atoms: 0.65 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: 0.59 Conformation dependent library (CDL) restraints added in 275.7 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: 0.15 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: 0.38 Time building geometry restraints manager: 0.68 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- 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 : 0.276 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: 0.1670 time to fit residues: 10.5149 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 : 0.330 ------------------------------------------------------------------------------- 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 = 0.079866 restraints weight = 8972.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.081645 restraints weight = 4744.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.082765 restraints weight = 2902.772| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.251 Fit side-chains REVERT: B 22 ASN cc_start: 0.8761 (p0) cc_final: 0.8560 (p0) REVERT: C 28 SER cc_start: 0.8758 (t) cc_final: 0.8557 (p) REVERT: E 27 LEU cc_start: 0.8865 (mp) cc_final: 0.8634 (mp) REVERT: G 28 SER cc_start: 0.9141 (t) cc_final: 0.8723 (p) REVERT: J 22 ASN cc_start: 0.7733 (p0) cc_final: 0.6995 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0848 time to fit residues: 4.3330 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 : 0.246 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN C 21 ASN C 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.083916 restraints weight = 9396.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.085625 restraints weight = 5204.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.086705 restraints weight = 3251.831| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2045 Z= 0.196 Angle : 0.745 9.609 2775 Z= 0.364 Chirality : 0.043 0.141 340 Planarity : 0.003 0.015 360 Dihedral : 6.911 22.059 275 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: -5.51 (0.31), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.24), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.011 0.002 PHE E 15 TYR 0.004 0.001 TYR E 37 ARG 0.003 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 39 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.295 Fit side-chains REVERT: E 32 VAL cc_start: 0.8179 (p) cc_final: 0.7687 (p) REVERT: G 28 SER cc_start: 0.9213 (t) cc_final: 0.8868 (p) REVERT: J 22 ASN cc_start: 0.7631 (p0) cc_final: 0.7035 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1119 time to fit residues: 5.6397 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 : 0.311 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.088501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080716 restraints weight = 9039.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082439 restraints weight = 4955.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.083621 restraints weight = 3131.932| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.003 0.025 2045 Z= 0.223 Angle : 0.739 9.627 2775 Z= 0.360 Chirality : 0.044 0.139 340 Planarity : 0.003 0.015 360 Dihedral : 6.956 20.660 275 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.30), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.31 (0.23), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 18 PHE 0.013 0.003 PHE J 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.001 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 33 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.219 Fit side-chains REVERT: E 10 GLN cc_start: 0.7871 (mp10) cc_final: 0.7470 (mp10) REVERT: J 22 ASN cc_start: 0.7851 (p0) cc_final: 0.6933 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0651 time to fit residues: 3.0760 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 : 0.222 ------------------------------------------------------------------------------- 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: 20.0000 chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 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 = 0.3865 r_free = 0.3865 target = 0.087683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080002 restraints weight = 9026.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.081512 restraints weight = 4844.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.082709 restraints weight = 3147.474| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2045 Z= 0.226 Angle : 0.753 10.093 2775 Z= 0.362 Chirality : 0.044 0.142 340 Planarity : 0.003 0.019 360 Dihedral : 6.964 20.447 275 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % 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: -5.84 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.44 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 18 PHE 0.012 0.003 PHE F 15 TYR 0.004 0.001 TYR E 37 ARG 0.003 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 33 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.256 Fit side-chains REVERT: E 10 GLN cc_start: 0.7950 (mp10) cc_final: 0.7533 (mp10) REVERT: J 22 ASN cc_start: 0.8025 (p0) cc_final: 0.6748 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0621 time to fit residues: 2.8957 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 : 0.210 ------------------------------------------------------------------------------- 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: 20.0000 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 40.0000 chunk 13 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS E 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080915 restraints weight = 9053.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082475 restraints weight = 4647.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.083639 restraints weight = 2973.992| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5188 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= 0.224 Angle : 0.745 10.701 2775 Z= 0.356 Chirality : 0.044 0.155 340 Planarity : 0.003 0.016 360 Dihedral : 7.006 24.473 275 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % 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: -5.91 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (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 H 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 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 : 0.245 Fit side-chains REVERT: E 10 GLN cc_start: 0.8084 (mp10) cc_final: 0.7773 (mp10) REVERT: J 22 ASN cc_start: 0.7811 (p0) cc_final: 0.6317 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0670 time to fit residues: 3.0267 Evaluate side-chains 22 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 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: 40.0000 chunk 11 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 0.0030 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.094389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.086860 restraints weight = 9051.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.088791 restraints weight = 4676.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.090016 restraints weight = 2820.617| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2045 Z= 0.195 Angle : 0.721 10.987 2775 Z= 0.346 Chirality : 0.044 0.138 340 Planarity : 0.002 0.012 360 Dihedral : 6.674 19.556 275 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -5.85 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 18 PHE 0.013 0.002 PHE D 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 35 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.190 Fit side-chains REVERT: E 10 GLN cc_start: 0.8036 (mp10) cc_final: 0.7693 (mp10) REVERT: E 21 ASN cc_start: 0.8217 (m110) cc_final: 0.7529 (m110) REVERT: J 22 ASN cc_start: 0.7805 (p0) cc_final: 0.6180 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0636 time to fit residues: 3.1110 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 : 0.251 ------------------------------------------------------------------------------- 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: 40.0000 chunk 5 optimal weight: 40.0000 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.095334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.087813 restraints weight = 10310.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.089500 restraints weight = 5102.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.090615 restraints weight = 3037.437| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2045 Z= 0.302 Angle : 0.793 9.778 2775 Z= 0.389 Chirality : 0.045 0.153 340 Planarity : 0.003 0.021 360 Dihedral : 7.398 21.666 275 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.47 % Favored : 83.53 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -6.02 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 18 PHE 0.015 0.003 PHE H 15 TYR 0.003 0.001 TYR E 37 ARG 0.003 0.001 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 29 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.228 Fit side-chains REVERT: E 10 GLN cc_start: 0.8256 (mp10) cc_final: 0.7831 (mp10) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0631 time to fit residues: 2.6430 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 : 0.238 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 40.0000 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.097475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.089853 restraints weight = 10176.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.091652 restraints weight = 5061.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.092807 restraints weight = 2981.342| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2045 Z= 0.218 Angle : 0.732 9.739 2775 Z= 0.353 Chirality : 0.044 0.148 340 Planarity : 0.002 0.014 360 Dihedral : 6.973 20.233 275 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -5.94 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 18 PHE 0.015 0.003 PHE E 15 TYR 0.003 0.001 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 30 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.324 Fit side-chains REVERT: E 10 GLN cc_start: 0.8144 (mp10) cc_final: 0.7748 (mp10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0793 time to fit residues: 3.3863 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 : 0.426 ------------------------------------------------------------------------------- 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: 50.0000 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 40.0000 chunk 13 optimal weight: 30.0000 chunk 3 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- 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 = 0.095585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.087974 restraints weight = 8906.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.089869 restraints weight = 4623.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091082 restraints weight = 2799.480| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2045 Z= 0.173 Angle : 0.698 9.652 2775 Z= 0.333 Chirality : 0.043 0.134 340 Planarity : 0.002 0.011 360 Dihedral : 6.444 19.477 275 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -5.84 (0.27), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.21), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.013 0.002 PHE G 15 TYR 0.003 0.000 TYR E 37 ARG 0.002 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 32 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.223 Fit side-chains REVERT: E 10 GLN cc_start: 0.8051 (mp10) cc_final: 0.7688 (mp10) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0610 time to fit residues: 2.7910 Evaluate side-chains 28 residues out of total 235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 40.0000 chunk 22 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 3 optimal weight: 0.0070 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 30.0000 overall best weight: 8.4008 ------------------------------------------------------------------------------- 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** G 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.085756 restraints weight = 9371.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.087464 restraints weight = 4922.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.088662 restraints weight = 3098.538| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2045 Z= 0.258 Angle : 0.756 8.889 2775 Z= 0.366 Chirality : 0.044 0.143 340 Planarity : 0.003 0.016 360 Dihedral : 7.010 19.383 275 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % 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: -5.99 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.20), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 18 PHE 0.015 0.003 PHE C 15 TYR 0.004 0.001 TYR E 37 ARG 0.003 0.000 ARG I 11 =============================================================================== Job complete usr+sys time: 914.59 seconds wall clock time: 16 minutes 50.54 seconds (1010.54 seconds total)