Starting phenix.real_space_refine on Fri May 9 14:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzs_35090/05_2025/8hzs_35090.cif" } resolution = 3.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 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 1488 2.51 5 N 408 2.21 5 O 480 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-5687/modules/chem_data/mon_lib" Total number of atoms: 2376 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.42, per 1000 atoms: 0.60 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 90.1, 30.74, 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 480 8.00 N 408 7.00 C 1488 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=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 368.9 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.367A pdb=" N LYS F 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.128A pdb=" N GLN F 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.362A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.129A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'E' and resid 81 through 82 20 hydrogen bonds defined for protein. 60 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: 0.48 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 414 1.29 - 1.35: 373 1.35 - 1.42: 102 1.42 - 1.48: 401 1.48 - 1.55: 1098 Bond restraints: 2388 Sorted by residual: bond pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.49e-01 bond pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.09e-01 bond pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.61e-01 bond pdb=" CA LEU D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.61e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.50e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 2730 0.68 - 1.36: 401 1.36 - 2.04: 85 2.04 - 2.72: 18 2.72 - 3.40: 6 Bond angle restraints: 3240 Sorted by residual: angle pdb=" CA ASN B 65 " pdb=" CB ASN B 65 " pdb=" CG ASN B 65 " ideal model delta sigma weight residual 112.60 114.52 -1.92 1.00e+00 1.00e+00 3.68e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.51 -1.91 1.00e+00 1.00e+00 3.64e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.55e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.54e+00 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 114.47 -1.87 1.00e+00 1.00e+00 3.50e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.23: 1206 12.23 - 24.45: 132 24.45 - 36.67: 18 36.67 - 48.90: 12 48.90 - 61.12: 6 Dihedral angle restraints: 1374 sinusoidal: 438 harmonic: 936 Sorted by residual: dihedral pdb=" CA VAL A 48 " pdb=" C VAL A 48 " pdb=" N VAL A 49 " pdb=" CA VAL A 49 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL B 48 " pdb=" C VAL B 48 " pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL F 48 " pdb=" C VAL F 48 " pdb=" N VAL F 49 " pdb=" CA VAL F 49 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 1371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 225 0.026 - 0.051: 100 0.051 - 0.076: 58 0.076 - 0.102: 35 0.102 - 0.127: 14 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA VAL D 70 " pdb=" N VAL D 70 " pdb=" C VAL D 70 " pdb=" CB VAL D 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA VAL F 70 " pdb=" N VAL F 70 " pdb=" C VAL F 70 " pdb=" CB VAL F 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.29e+00 pdb=" C SER E 87 " 0.020 2.00e-02 2.50e+03 pdb=" O SER E 87 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE E 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 87 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C SER C 87 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 88 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 87 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C SER F 87 " -0.019 2.00e-02 2.50e+03 pdb=" O SER F 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE F 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 331 2.77 - 3.30: 2210 3.30 - 3.83: 3523 3.83 - 4.37: 3820 4.37 - 4.90: 7885 Nonbonded interactions: 17769 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU B 61 " pdb=" OG1 THR B 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU C 61 " pdb=" OG1 THR C 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU D 61 " pdb=" OG1 THR D 72 " model vdw 2.235 3.040 ... (remaining 17764 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 'F' } 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 individual isotropic 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: 0.970 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.003 0.024 2388 Z= 0.144 Angle : 0.545 3.397 3240 Z= 0.315 Chirality : 0.045 0.127 432 Planarity : 0.002 0.011 402 Dihedral : 11.889 61.125 786 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % 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: -5.68 (0.26), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.20), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.001 0.000 PHE F 94 TYR 0.002 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.11588 ( 20) hydrogen bonds : angle 7.71489 ( 60) covalent geometry : bond 0.00310 ( 2388) covalent geometry : angle 0.54533 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.229 Fit side-chains REVERT: C 83 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7380 (mm-30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0794 time to fit residues: 2.8303 Evaluate side-chains 25 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.162688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.139272 restraints weight = 2763.237| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.76 r_work: 0.3957 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 2388 Z= 0.300 Angle : 0.686 4.782 3240 Z= 0.382 Chirality : 0.047 0.133 432 Planarity : 0.003 0.012 402 Dihedral : 5.543 16.378 348 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % Rotamer: Outliers : 9.17 % Allowed : 12.08 % Favored : 78.75 % 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: -5.52 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.20 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.005 0.001 PHE B 94 TYR 0.006 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 20) hydrogen bonds : angle 6.66280 ( 60) covalent geometry : bond 0.00705 ( 2388) covalent geometry : angle 0.68565 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.231 Fit side-chains REVERT: A 42 SER cc_start: 0.9074 (p) cc_final: 0.8733 (m) outliers start: 22 outliers final: 20 residues processed: 47 average time/residue: 0.0652 time to fit residues: 4.2912 Evaluate side-chains 51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.170513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.146902 restraints weight = 2661.927| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.70 r_work: 0.4080 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2388 Z= 0.139 Angle : 0.535 5.659 3240 Z= 0.299 Chirality : 0.045 0.159 432 Planarity : 0.002 0.010 402 Dihedral : 4.936 17.147 348 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.42 % Allowed : 19.58 % Favored : 75.00 % 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: -4.81 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.002 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 20) hydrogen bonds : angle 6.25948 ( 60) covalent geometry : bond 0.00326 ( 2388) covalent geometry : angle 0.53503 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.248 Fit side-chains REVERT: A 71 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (t) outliers start: 13 outliers final: 8 residues processed: 34 average time/residue: 0.0676 time to fit residues: 3.4175 Evaluate side-chains 32 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 0.0370 overall best weight: 2.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.168321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.144379 restraints weight = 2649.412| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.73 r_work: 0.4031 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2388 Z= 0.193 Angle : 0.565 3.944 3240 Z= 0.317 Chirality : 0.048 0.165 432 Planarity : 0.002 0.011 402 Dihedral : 4.958 16.975 348 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 8.75 % Allowed : 16.25 % Favored : 75.00 % 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: -4.56 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.003 0.001 PHE B 94 TYR 0.003 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 20) hydrogen bonds : angle 6.07928 ( 60) covalent geometry : bond 0.00457 ( 2388) covalent geometry : angle 0.56518 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 21 time to evaluate : 0.262 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 37 average time/residue: 0.0677 time to fit residues: 3.6368 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.7484 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.171062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.147040 restraints weight = 2687.764| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.72 r_work: 0.4073 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2388 Z= 0.156 Angle : 0.585 6.365 3240 Z= 0.321 Chirality : 0.048 0.168 432 Planarity : 0.002 0.012 402 Dihedral : 4.805 17.182 348 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 11.67 % Allowed : 12.50 % Favored : 75.83 % 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: -4.25 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.001 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 20) hydrogen bonds : angle 5.76148 ( 60) covalent geometry : bond 0.00366 ( 2388) covalent geometry : angle 0.58479 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 22 time to evaluate : 0.249 Fit side-chains REVERT: F 38 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (tt) REVERT: F 62 GLN cc_start: 0.8136 (tt0) cc_final: 0.7797 (mt0) REVERT: E 65 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7746 (t0) outliers start: 28 outliers final: 17 residues processed: 42 average time/residue: 0.0640 time to fit residues: 3.8858 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 21 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.166971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143036 restraints weight = 2665.359| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.73 r_work: 0.4010 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 2388 Z= 0.253 Angle : 0.693 6.699 3240 Z= 0.384 Chirality : 0.049 0.156 432 Planarity : 0.003 0.015 402 Dihedral : 5.301 16.830 348 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 10.00 % Allowed : 12.08 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.003 0.001 PHE B 94 TYR 0.005 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 20) hydrogen bonds : angle 5.94397 ( 60) covalent geometry : bond 0.00597 ( 2388) covalent geometry : angle 0.69299 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 26 time to evaluate : 0.233 Fit side-chains REVERT: F 38 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8636 (tt) REVERT: F 62 GLN cc_start: 0.8233 (tt0) cc_final: 0.7908 (mt0) REVERT: F 83 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 83 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7982 (mm-30) REVERT: A 42 SER cc_start: 0.9028 (p) cc_final: 0.8723 (m) outliers start: 24 outliers final: 22 residues processed: 46 average time/residue: 0.0656 time to fit residues: 4.2236 Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.180685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.157053 restraints weight = 2637.494| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.61 r_work: 0.4194 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2388 Z= 0.093 Angle : 0.552 7.568 3240 Z= 0.298 Chirality : 0.048 0.158 432 Planarity : 0.003 0.021 402 Dihedral : 4.364 16.874 348 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 6.25 % Allowed : 16.25 % Favored : 77.50 % 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 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.002 0.000 PHE D 94 TYR 0.003 0.000 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 20) hydrogen bonds : angle 5.36894 ( 60) covalent geometry : bond 0.00197 ( 2388) covalent geometry : angle 0.55198 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.230 Fit side-chains REVERT: F 62 GLN cc_start: 0.7998 (tt0) cc_final: 0.7754 (mt0) REVERT: E 62 GLN cc_start: 0.8117 (tt0) cc_final: 0.7386 (mt0) outliers start: 15 outliers final: 10 residues processed: 29 average time/residue: 0.0658 time to fit residues: 2.8100 Evaluate side-chains 26 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 16 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.173961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.150675 restraints weight = 2707.241| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.63 r_work: 0.4133 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2388 Z= 0.136 Angle : 0.565 7.293 3240 Z= 0.297 Chirality : 0.047 0.122 432 Planarity : 0.003 0.020 402 Dihedral : 4.505 16.454 348 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 5.42 % Allowed : 14.58 % 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: -3.81 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.001 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 20) hydrogen bonds : angle 5.17305 ( 60) covalent geometry : bond 0.00308 ( 2388) covalent geometry : angle 0.56469 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 13 time to evaluate : 0.239 Fit side-chains REVERT: C 42 SER cc_start: 0.9015 (p) cc_final: 0.8749 (m) REVERT: E 62 GLN cc_start: 0.8080 (tt0) cc_final: 0.7360 (mt0) outliers start: 13 outliers final: 13 residues processed: 25 average time/residue: 0.0710 time to fit residues: 2.6369 Evaluate side-chains 26 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 13 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 0.0070 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.171286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.147854 restraints weight = 2716.804| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.69 r_work: 0.4091 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2388 Z= 0.178 Angle : 0.603 7.349 3240 Z= 0.322 Chirality : 0.047 0.125 432 Planarity : 0.003 0.020 402 Dihedral : 4.878 16.555 348 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 7.50 % Allowed : 12.92 % Favored : 79.58 % 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: -3.78 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.001 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 20) hydrogen bonds : angle 5.36945 ( 60) covalent geometry : bond 0.00411 ( 2388) covalent geometry : angle 0.60254 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 11 time to evaluate : 0.246 Fit side-chains REVERT: C 83 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 65 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7840 (t0) outliers start: 18 outliers final: 17 residues processed: 28 average time/residue: 0.0683 time to fit residues: 2.8333 Evaluate side-chains 29 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 11 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.140255 restraints weight = 2622.841| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.75 r_work: 0.3886 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2388 Z= 0.279 Angle : 0.727 7.843 3240 Z= 0.387 Chirality : 0.049 0.128 432 Planarity : 0.003 0.020 402 Dihedral : 5.419 16.309 348 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 7.92 % Allowed : 12.92 % Favored : 79.17 % 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: -3.94 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.003 0.000 PHE D 94 TYR 0.007 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 20) hydrogen bonds : angle 5.56967 ( 60) covalent geometry : bond 0.00647 ( 2388) covalent geometry : angle 0.72701 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 20 time to evaluate : 0.261 Fit side-chains REVERT: F 83 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 83 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7726 (mm-30) outliers start: 19 outliers final: 18 residues processed: 37 average time/residue: 0.0703 time to fit residues: 3.6940 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 19 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.171808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.148770 restraints weight = 2669.807| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.63 r_work: 0.4098 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2388 Z= 0.160 Angle : 0.625 7.435 3240 Z= 0.334 Chirality : 0.047 0.127 432 Planarity : 0.003 0.020 402 Dihedral : 4.995 16.339 348 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 6.25 % Allowed : 15.00 % Favored : 78.75 % 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: -3.80 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.003 0.000 PHE B 94 TYR 0.003 0.001 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 20) hydrogen bonds : angle 5.23932 ( 60) covalent geometry : bond 0.00365 ( 2388) covalent geometry : angle 0.62468 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.46 seconds wall clock time: 25 minutes 20.42 seconds (1520.42 seconds total)