Starting phenix.real_space_refine on Wed Jul 23 07:03:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.map" model { file = "/net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m64_23688/07_2025/7m64_23688.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1140 2.51 5 N 330 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 1850 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 0.87, per 1000 atoms: 0.47 Number of scatterers: 1850 At special positions: 0 Unit cell: (48.53, 66.465, 44.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 380 8.00 N 330 7.00 C 1140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 256.5 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.145A pdb=" N PHE D 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE A 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE E 15 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE I 15 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU A 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU E 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.570A pdb=" N PHE G 15 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 15 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE F 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.871A pdb=" N LEU C 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 27 " --> pdb=" O SER C 28 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.42 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 300 1.29 - 1.36: 313 1.36 - 1.43: 267 1.43 - 1.50: 297 1.50 - 1.56: 693 Bond restraints: 1870 Sorted by residual: bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.32e+00 bond pdb=" C ALA C 13 " pdb=" N ASN C 14 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.25e-02 6.40e+03 4.29e+00 bond pdb=" N ALA F 13 " pdb=" CA ALA F 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" N ALA H 13 " pdb=" CA ALA H 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 ... (remaining 1865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 1993 1.17 - 2.34: 385 2.34 - 3.51: 114 3.51 - 4.68: 38 4.68 - 5.85: 10 Bond angle restraints: 2540 Sorted by residual: angle pdb=" C ALA H 13 " pdb=" CA ALA H 13 " pdb=" CB ALA H 13 " ideal model delta sigma weight residual 110.50 116.35 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta sigma weight residual 110.50 116.34 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA B 13 " pdb=" CA ALA B 13 " pdb=" CB ALA B 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA F 13 " pdb=" CA ALA F 13 " pdb=" CB ALA F 13 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 2535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.60: 760 5.60 - 11.20: 140 11.20 - 16.80: 59 16.80 - 22.40: 61 22.40 - 27.99: 20 Dihedral angle restraints: 1040 sinusoidal: 330 harmonic: 710 Sorted by residual: dihedral pdb=" C ALA J 13 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " pdb=" CB ALA J 13 " ideal model delta harmonic sigma weight residual -122.60 -132.53 9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" C ALA C 13 " pdb=" N ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C ALA E 13 " pdb=" N ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta harmonic sigma weight residual -122.60 -132.49 9.89 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 224 0.045 - 0.090: 36 0.090 - 0.135: 11 0.135 - 0.179: 9 0.179 - 0.224: 20 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ALA J 13 " pdb=" N ALA J 13 " pdb=" C ALA J 13 " pdb=" CB ALA J 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA C 13 " pdb=" N ALA C 13 " pdb=" C ALA C 13 " pdb=" CB ALA C 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA G 13 " pdb=" N ALA G 13 " pdb=" C ALA G 13 " pdb=" CB ALA G 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 297 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 13 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA F 13 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA F 13 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN F 14 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 13 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA C 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 13 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA H 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA H 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN H 14 " -0.008 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 998 2.94 - 3.43: 2256 3.43 - 3.92: 2945 3.92 - 4.41: 3321 4.41 - 4.90: 6387 Nonbonded interactions: 15907 Sorted by model distance: nonbonded pdb=" OG SER I 19 " pdb=" OD1 ASN I 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER A 19 " pdb=" OD1 ASN A 22 " model vdw 2.451 3.040 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.451 3.040 ... (remaining 15902 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 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' 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: 0.240 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.240 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.011 0.103 1880 Z= 0.868 Angle : 1.155 5.847 2540 Z= 0.676 Chirality : 0.068 0.224 300 Planarity : 0.004 0.013 330 Dihedral : 10.068 27.994 580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -3.84 (0.40), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.009 0.002 PHE F 23 TYR 0.003 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.32077 ( 12) hydrogen bonds : angle 10.76712 ( 36) covalent geometry : bond 0.00801 ( 1870) covalent geometry : angle 1.15497 ( 2540) Misc. bond : bond 0.10271 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0721 time to fit residues: 2.9258 Evaluate side-chains 25 residues out of total 210 (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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.098803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.089021 restraints weight = 6386.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090969 restraints weight = 3407.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.092345 restraints weight = 2131.597| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1880 Z= 0.198 Angle : 0.857 7.177 2540 Z= 0.435 Chirality : 0.046 0.125 300 Planarity : 0.003 0.009 330 Dihedral : 4.457 13.633 250 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 13.33 % Favored : 86.19 % 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: -4.01 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.010 0.002 PHE H 23 TYR 0.006 0.001 TYR J 37 Details of bonding type rmsd hydrogen bonds : bond 0.06133 ( 12) hydrogen bonds : angle 6.26392 ( 36) covalent geometry : bond 0.00378 ( 1870) covalent geometry : angle 0.85718 ( 2540) Misc. bond : bond 0.00053 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.230 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0669 time to fit residues: 2.4566 Evaluate side-chains 26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.097852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.088092 restraints weight = 6380.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.089983 restraints weight = 3384.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.091155 restraints weight = 2127.513| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1880 Z= 0.196 Angle : 0.822 7.045 2540 Z= 0.419 Chirality : 0.047 0.165 300 Planarity : 0.002 0.009 330 Dihedral : 4.407 11.481 250 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 15.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 18 PHE 0.012 0.002 PHE C 15 TYR 0.008 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 12) hydrogen bonds : angle 5.99547 ( 36) covalent geometry : bond 0.00376 ( 1870) covalent geometry : angle 0.82230 ( 2540) Misc. bond : bond 0.00034 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.223 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.0740 time to fit residues: 2.1463 Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.096692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.086756 restraints weight = 6451.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088638 restraints weight = 3427.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.089914 restraints weight = 2172.893| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1880 Z= 0.222 Angle : 0.839 6.398 2540 Z= 0.426 Chirality : 0.046 0.137 300 Planarity : 0.003 0.010 330 Dihedral : 4.703 12.890 250 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 18 PHE 0.011 0.002 PHE C 15 TYR 0.007 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 12) hydrogen bonds : angle 5.87938 ( 36) covalent geometry : bond 0.00430 ( 1870) covalent geometry : angle 0.83911 ( 2540) Misc. bond : bond 0.00039 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.216 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 18 average time/residue: 0.0732 time to fit residues: 1.9497 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN I 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.089216 restraints weight = 6402.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.091240 restraints weight = 3368.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.092432 restraints weight = 2103.453| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1880 Z= 0.164 Angle : 0.776 6.146 2540 Z= 0.390 Chirality : 0.045 0.135 300 Planarity : 0.002 0.011 330 Dihedral : 4.472 12.776 250 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.35), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.27), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 18 PHE 0.010 0.002 PHE C 15 TYR 0.003 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 12) hydrogen bonds : angle 5.55975 ( 36) covalent geometry : bond 0.00317 ( 1870) covalent geometry : angle 0.77588 ( 2540) Misc. bond : bond 0.00035 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.205 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 20 average time/residue: 0.0641 time to fit residues: 1.8968 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088965 restraints weight = 6529.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090947 restraints weight = 3433.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.092167 restraints weight = 2151.182| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1880 Z= 0.183 Angle : 0.806 8.578 2540 Z= 0.403 Chirality : 0.045 0.138 300 Planarity : 0.002 0.010 330 Dihedral : 4.585 13.145 250 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 19.52 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.35), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 18 PHE 0.011 0.002 PHE C 15 TYR 0.005 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 12) hydrogen bonds : angle 5.59828 ( 36) covalent geometry : bond 0.00354 ( 1870) covalent geometry : angle 0.80606 ( 2540) Misc. bond : bond 0.00028 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.199 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0547 time to fit residues: 1.5327 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.100393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.090246 restraints weight = 6305.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.092180 restraints weight = 3377.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.093545 restraints weight = 2162.098| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1880 Z= 0.165 Angle : 0.784 8.126 2540 Z= 0.388 Chirality : 0.044 0.136 300 Planarity : 0.002 0.010 330 Dihedral : 4.478 13.298 250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 18.57 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.002 PHE E 15 TYR 0.004 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 12) hydrogen bonds : angle 5.58083 ( 36) covalent geometry : bond 0.00317 ( 1870) covalent geometry : angle 0.78415 ( 2540) Misc. bond : bond 0.00023 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.223 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.0641 time to fit residues: 1.9105 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 0.0060 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 overall best weight: 6.6004 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.100084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.089486 restraints weight = 6193.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.091542 restraints weight = 3187.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.093020 restraints weight = 1992.073| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1880 Z= 0.170 Angle : 0.799 8.261 2540 Z= 0.396 Chirality : 0.044 0.135 300 Planarity : 0.002 0.013 330 Dihedral : 4.547 12.956 250 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 19.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.002 PHE E 15 TYR 0.006 0.001 TYR I 37 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 12) hydrogen bonds : angle 5.40909 ( 36) covalent geometry : bond 0.00330 ( 1870) covalent geometry : angle 0.79870 ( 2540) Misc. bond : bond 0.00025 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.225 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0704 time to fit residues: 1.7355 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.097826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.087224 restraints weight = 6440.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.089177 restraints weight = 3321.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.090500 restraints weight = 2103.494| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1880 Z= 0.204 Angle : 0.831 8.221 2540 Z= 0.416 Chirality : 0.045 0.137 300 Planarity : 0.003 0.012 330 Dihedral : 4.786 13.488 250 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.43 % Allowed : 19.05 % Favored : 79.52 % 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: -3.87 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 18 PHE 0.010 0.002 PHE C 15 TYR 0.006 0.001 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 12) hydrogen bonds : angle 5.60504 ( 36) covalent geometry : bond 0.00398 ( 1870) covalent geometry : angle 0.83129 ( 2540) Misc. bond : bond 0.00032 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.220 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0683 time to fit residues: 1.7459 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 0.0870 chunk 3 optimal weight: 7.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.090411 restraints weight = 6154.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.092463 restraints weight = 3130.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.093828 restraints weight = 1950.875| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1880 Z= 0.130 Angle : 0.768 8.253 2540 Z= 0.373 Chirality : 0.044 0.130 300 Planarity : 0.002 0.011 330 Dihedral : 4.511 13.456 250 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.48 % Allowed : 19.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.008 0.001 PHE E 15 TYR 0.003 0.000 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 12) hydrogen bonds : angle 5.39228 ( 36) covalent geometry : bond 0.00251 ( 1870) covalent geometry : angle 0.76782 ( 2540) Misc. bond : bond 0.00018 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.255 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0767 time to fit residues: 1.9728 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 14 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 overall best weight: 6.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.098359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.088535 restraints weight = 6177.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.090476 restraints weight = 3020.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.091876 restraints weight = 1884.817| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1880 Z= 0.168 Angle : 0.795 8.390 2540 Z= 0.393 Chirality : 0.044 0.132 300 Planarity : 0.002 0.010 330 Dihedral : 4.550 13.580 250 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.95 % Allowed : 19.05 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.34), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.26), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 18 PHE 0.009 0.002 PHE C 15 TYR 0.005 0.001 TYR D 37 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 12) hydrogen bonds : angle 5.24364 ( 36) covalent geometry : bond 0.00324 ( 1870) covalent geometry : angle 0.79545 ( 2540) Misc. bond : bond 0.00022 ( 10) =============================================================================== Job complete usr+sys time: 848.05 seconds wall clock time: 15 minutes 45.91 seconds (945.91 seconds total)