Starting phenix.real_space_refine on Wed Mar 5 15:34:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4d_31708/03_2025/7v4d_31708.cif" } resolution = 3.5 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-5624/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: 1.86, per 1000 atoms: 0.78 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 87.98, 31.8, 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: 0.57 Conformation dependent library (CDL) restraints added in 326.3 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: 0.37 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: 6.361A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.360A 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: 6.189A 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: 0.50 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.42e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.17e-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 9.07e-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 9.04e-01 bond pdb=" CA LEU C 38 " pdb=" C LEU C 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.62e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 2731 0.68 - 1.36: 401 1.36 - 2.04: 84 2.04 - 2.72: 18 2.72 - 3.41: 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 3.70e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.48 -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 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.52e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.21: 1206 12.21 - 24.43: 132 24.43 - 36.64: 18 36.64 - 48.85: 12 48.85 - 61.07: 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 180.00 162.67 17.33 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 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 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 - 0.025: 214 0.025 - 0.049: 108 0.049 - 0.074: 52 0.074 - 0.099: 34 0.099 - 0.124: 24 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 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 2.56 -0.12 2.00e-01 2.50e+01 3.81e-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 3.62e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 87 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+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 E 87 " -0.006 2.00e-02 2.50e+03 1.14e-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 F 87 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+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: 2209 3.30 - 3.83: 3524 3.83 - 4.37: 3821 4.37 - 4.90: 7885 Nonbonded interactions: 17770 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 72 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLU E 61 " pdb=" OG1 THR E 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 B 61 " pdb=" OG1 THR B 72 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 3.040 ... (remaining 17765 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 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: 0.960 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.320 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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= 0.196 Angle : 0.544 3.405 3240 Z= 0.315 Chirality : 0.045 0.124 432 Planarity : 0.002 0.011 402 Dihedral : 11.888 61.066 786 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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: -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 F 50 PHE 0.001 0.000 PHE F 94 TYR 0.002 0.001 TYR B 39 *********************** 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 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.242 Fit side-chains REVERT: F 83 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7835 (pm20) REVERT: C 46 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 83 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7843 (mm-30) REVERT: B 62 GLN cc_start: 0.8139 (tt0) cc_final: 0.7757 (tt0) REVERT: B 83 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7599 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0767 time to fit residues: 4.1917 Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.164468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135952 restraints weight = 2665.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.139270 restraints weight = 1365.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.141564 restraints weight = 948.262| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2388 Z= 0.332 Angle : 0.634 5.466 3240 Z= 0.346 Chirality : 0.047 0.134 432 Planarity : 0.003 0.012 402 Dihedral : 5.373 16.509 348 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % 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: -5.32 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.005 0.001 PHE D 94 TYR 0.004 0.002 TYR D 39 *********************** 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 55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.239 Fit side-chains REVERT: F 83 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7630 (pm20) REVERT: C 46 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7968 (mt-10) REVERT: C 83 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7883 (mm-30) REVERT: E 79 GLN cc_start: 0.8263 (mt0) cc_final: 0.7999 (mt0) outliers start: 18 outliers final: 11 residues processed: 52 average time/residue: 0.0745 time to fit residues: 5.2711 Evaluate side-chains 47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER 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: 0.9980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.168980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.140426 restraints weight = 2600.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.143909 restraints weight = 1281.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.146166 restraints weight = 872.961| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2388 Z= 0.305 Angle : 0.631 4.922 3240 Z= 0.348 Chirality : 0.047 0.134 432 Planarity : 0.003 0.014 402 Dihedral : 5.356 16.677 348 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 9.58 % Allowed : 15.83 % Favored : 74.58 % 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: -5.00 (0.31), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE D 94 TYR 0.004 0.001 TYR B 39 *********************** 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 61 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.261 Fit side-chains REVERT: F 83 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7666 (pm20) REVERT: C 46 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 83 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7964 (mm-30) outliers start: 23 outliers final: 20 residues processed: 52 average time/residue: 0.0685 time to fit residues: 4.9231 Evaluate side-chains 57 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.163430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.135033 restraints weight = 2655.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138252 restraints weight = 1392.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140629 restraints weight = 979.108| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2388 Z= 0.421 Angle : 0.708 5.331 3240 Z= 0.385 Chirality : 0.047 0.137 432 Planarity : 0.003 0.014 402 Dihedral : 5.714 16.301 348 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 11.25 % Allowed : 12.92 % 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: -5.02 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.006 0.001 PHE D 94 TYR 0.005 0.002 TYR B 39 *********************** 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 60 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 33 time to evaluate : 0.270 Fit side-chains REVERT: F 83 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7718 (pm20) REVERT: C 46 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8053 (mt-10) REVERT: C 83 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 62 GLN cc_start: 0.8244 (tt0) cc_final: 0.7894 (tt0) outliers start: 27 outliers final: 23 residues processed: 51 average time/residue: 0.0698 time to fit residues: 4.9160 Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 46 GLU 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: 1.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4659 r_free = 0.4659 target = 0.182410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.154542 restraints weight = 2603.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.157784 restraints weight = 1390.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.159967 restraints weight = 979.440| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2388 Z= 0.162 Angle : 0.571 4.979 3240 Z= 0.316 Chirality : 0.047 0.126 432 Planarity : 0.002 0.012 402 Dihedral : 4.909 16.134 348 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 7.08 % Allowed : 16.67 % Favored : 76.25 % 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: -4.48 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.26), 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 0.001 0.000 TYR E 39 *********************** 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 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.248 Fit side-chains REVERT: F 83 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7726 (pm20) REVERT: C 46 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7947 (mt-10) outliers start: 17 outliers final: 12 residues processed: 48 average time/residue: 0.0729 time to fit residues: 4.8264 Evaluate side-chains 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain B residue 46 GLU 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: 7.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.161516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.135168 restraints weight = 2745.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.138248 restraints weight = 1476.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.140252 restraints weight = 1032.553| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 2388 Z= 0.496 Angle : 0.756 7.093 3240 Z= 0.411 Chirality : 0.049 0.142 432 Planarity : 0.003 0.016 402 Dihedral : 5.825 16.222 348 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 9.58 % Allowed : 13.33 % Favored : 77.08 % 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: -4.74 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.002 PHE D 94 TYR 0.005 0.002 TYR B 39 *********************** 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 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.248 Fit side-chains REVERT: C 46 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 62 GLN cc_start: 0.8172 (tt0) cc_final: 0.7869 (tt0) outliers start: 23 outliers final: 20 residues processed: 51 average time/residue: 0.0738 time to fit residues: 5.1803 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E 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 A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4614 r_free = 0.4614 target = 0.173465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.145921 restraints weight = 2741.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.149435 restraints weight = 1421.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.151646 restraints weight = 965.712| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2388 Z= 0.185 Angle : 0.619 6.670 3240 Z= 0.341 Chirality : 0.048 0.126 432 Planarity : 0.002 0.013 402 Dihedral : 4.986 15.652 348 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.67 % Allowed : 18.33 % 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: -4.27 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.003 0.001 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** 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 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.251 Fit side-chains REVERT: C 46 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7976 (mt-10) outliers start: 16 outliers final: 14 residues processed: 46 average time/residue: 0.0713 time to fit residues: 4.5375 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain B residue 46 GLU 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: 7.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.4582 ------------------------------------------------------------------------------- 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 = 0.4734 r_free = 0.4734 target = 0.187836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.159937 restraints weight = 2597.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.163346 restraints weight = 1344.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.165531 restraints weight = 932.675| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2388 Z= 0.139 Angle : 0.559 8.186 3240 Z= 0.298 Chirality : 0.048 0.125 432 Planarity : 0.003 0.021 402 Dihedral : 4.399 15.852 348 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 6.25 % Allowed : 16.67 % Favored : 77.08 % 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: -3.83 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.002 0.000 PHE B 94 TYR 0.003 0.001 TYR B 39 *********************** 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 48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.200 Fit side-chains REVERT: F 38 LEU cc_start: 0.9146 (tp) cc_final: 0.8886 (tp) REVERT: C 46 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7838 (mt-10) outliers start: 15 outliers final: 9 residues processed: 46 average time/residue: 0.0663 time to fit residues: 4.2439 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL 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: 7.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 3 optimal weight: 0.0010 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 0.5324 ------------------------------------------------------------------------------- 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 = 0.4749 r_free = 0.4749 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.159729 restraints weight = 2519.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.163187 restraints weight = 1269.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.165391 restraints weight = 869.808| |-----------------------------------------------------------------------------| r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2388 Z= 0.158 Angle : 0.558 7.653 3240 Z= 0.299 Chirality : 0.047 0.126 432 Planarity : 0.003 0.019 402 Dihedral : 4.311 15.852 348 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.58 % Allowed : 17.08 % Favored : 78.33 % 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: -3.55 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.002 0.000 PHE D 94 TYR 0.002 0.001 TYR A 39 *********************** 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 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.257 Fit side-chains REVERT: F 38 LEU cc_start: 0.9142 (tp) cc_final: 0.8880 (tp) REVERT: C 46 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7842 (mt-10) outliers start: 11 outliers final: 10 residues processed: 41 average time/residue: 0.0719 time to fit residues: 4.1466 Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain B residue 46 GLU 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: 5.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 = 0.4683 r_free = 0.4683 target = 0.181148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.154630 restraints weight = 2550.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.157954 restraints weight = 1307.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.160195 restraints weight = 898.780| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.003 0.028 2388 Z= 0.214 Angle : 0.585 8.282 3240 Z= 0.311 Chirality : 0.047 0.125 432 Planarity : 0.003 0.020 402 Dihedral : 4.576 16.060 348 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.58 % Allowed : 17.92 % 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: -3.43 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE C 94 TYR 0.002 0.001 TYR F 39 ********************** 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 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.252 Fit side-chains REVERT: F 38 LEU cc_start: 0.9148 (tp) cc_final: 0.8862 (tp) REVERT: C 46 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 11 outliers final: 11 residues processed: 35 average time/residue: 0.0768 time to fit residues: 3.7670 Evaluate side-chains 37 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 46 GLU 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: 5.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4628 r_free = 0.4628 target = 0.172616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.145049 restraints weight = 2669.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.148471 restraints weight = 1387.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.150711 restraints weight = 958.674| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2388 Z= 0.244 Angle : 0.604 8.247 3240 Z= 0.322 Chirality : 0.047 0.127 432 Planarity : 0.003 0.020 402 Dihedral : 4.822 16.074 348 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 5.42 % Allowed : 17.08 % 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: -3.45 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.003 0.001 PHE E 94 TYR 0.003 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.61 seconds wall clock time: 20 minutes 50.41 seconds (1250.41 seconds total)