Starting phenix.real_space_refine on Mon Feb 10 23:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.map" model { file = "/net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlx_22383/02_2025/7jlx_22383.cif" } resolution = 4.6 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 1960 2.51 5 N 664 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3288 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 822 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 2, 'TRANS': 163} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 315 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 822 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 2, 'TRANS': 163} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 315 Restraints were copied for chains: B, D Time building chain proxies: 4.81, per 1000 atoms: 1.46 Number of scatterers: 3288 At special positions: 0 Unit cell: (95.7372, 93.86, 53.5002, 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 664 8.00 N 664 7.00 C 1960 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: 1.08 Conformation dependent library (CDL) restraints added in 690.9 milliseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 57.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.523A pdb=" N ILE B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 80 through 97 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.635A pdb=" N ARG C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.446A pdb=" N PHE C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 39 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.524A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.634A pdb=" N ARG D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 4.447A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.835A pdb=" N VAL B 70 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 72 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 102 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 71 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.649A pdb=" N VAL C 70 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 71 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS C 154 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.835A pdb=" N VAL A 70 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 72 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 102 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 71 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 14 through 17 removed outlier: 3.649A pdb=" N VAL D 70 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 71 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS D 154 " --> pdb=" O VAL D 101 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 804 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: 0.87 Time building geometry restraints manager: 1.19 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: 664 1.29 - 1.36: 660 1.36 - 1.42: 0 1.42 - 1.48: 664 1.48 - 1.55: 1296 Bond restraints: 3284 Sorted by residual: bond pdb=" C VAL B 102 " pdb=" O VAL B 102 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.57e-01 bond pdb=" C VAL A 102 " pdb=" O VAL A 102 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.58e-01 bond pdb=" CA ASP D 163 " pdb=" C ASP D 163 " ideal model delta sigma weight residual 1.523 1.517 0.006 1.10e-02 8.26e+03 2.83e-01 bond pdb=" CA VAL B 102 " pdb=" CB VAL B 102 " ideal model delta sigma weight residual 1.540 1.535 0.005 9.00e-03 1.23e+04 2.77e-01 bond pdb=" CA ASP C 163 " pdb=" C ASP C 163 " ideal model delta sigma weight residual 1.523 1.517 0.006 1.10e-02 8.26e+03 2.60e-01 ... (remaining 3279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 4421 0.97 - 1.95: 132 1.95 - 2.92: 11 2.92 - 3.89: 6 3.89 - 4.87: 2 Bond angle restraints: 4572 Sorted by residual: angle pdb=" N LYS D 47 " pdb=" CA LYS D 47 " pdb=" C LYS D 47 " ideal model delta sigma weight residual 114.04 110.39 3.65 1.24e+00 6.50e-01 8.66e+00 angle pdb=" N LYS C 47 " pdb=" CA LYS C 47 " pdb=" C LYS C 47 " ideal model delta sigma weight residual 114.04 110.41 3.63 1.24e+00 6.50e-01 8.56e+00 angle pdb=" C TYR A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta sigma weight residual 121.54 126.41 -4.87 1.91e+00 2.74e-01 6.50e+00 angle pdb=" C TYR B 160 " pdb=" N ASN B 161 " pdb=" CA ASN B 161 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.22e+00 angle pdb=" N ASP D 45 " pdb=" CA ASP D 45 " pdb=" C ASP D 45 " ideal model delta sigma weight residual 113.20 109.98 3.22 1.36e+00 5.41e-01 5.61e+00 ... (remaining 4567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 2.66: 1647 2.66 - 5.32: 169 5.32 - 7.97: 74 7.97 - 10.63: 28 10.63 - 13.29: 6 Dihedral angle restraints: 1924 sinusoidal: 0 harmonic: 1924 Sorted by residual: dihedral pdb=" CA TYR D 160 " pdb=" C TYR D 160 " pdb=" N ASN D 161 " pdb=" CA ASN D 161 " ideal model delta harmonic sigma weight residual 180.00 166.71 13.29 0 5.00e+00 4.00e-02 7.06e+00 dihedral pdb=" CA TYR C 160 " pdb=" C TYR C 160 " pdb=" N ASN C 161 " pdb=" CA ASN C 161 " ideal model delta harmonic sigma weight residual 180.00 166.74 13.26 0 5.00e+00 4.00e-02 7.03e+00 dihedral pdb=" CA THR C 26 " pdb=" C THR C 26 " pdb=" N PHE C 27 " pdb=" CA PHE C 27 " ideal model delta harmonic sigma weight residual -180.00 -169.05 -10.95 0 5.00e+00 4.00e-02 4.80e+00 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.025: 362 0.025 - 0.049: 124 0.049 - 0.073: 85 0.073 - 0.097: 22 0.097 - 0.121: 39 Chirality restraints: 632 Sorted by residual: chirality pdb=" CA VAL D 104 " pdb=" N VAL D 104 " pdb=" C VAL D 104 " pdb=" CB VAL D 104 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 629 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 76 " -0.003 2.00e-02 2.50e+03 5.65e-03 3.19e-01 pdb=" C ASN B 76 " 0.010 2.00e-02 2.50e+03 pdb=" O ASN B 76 " -0.004 2.00e-02 2.50e+03 pdb=" N TYR B 77 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 76 " 0.003 2.00e-02 2.50e+03 5.57e-03 3.10e-01 pdb=" C ASN A 76 " -0.010 2.00e-02 2.50e+03 pdb=" O ASN A 76 " 0.004 2.00e-02 2.50e+03 pdb=" N TYR A 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 135 " -0.002 2.00e-02 2.50e+03 4.33e-03 1.87e-01 pdb=" C ARG D 135 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG D 135 " -0.003 2.00e-02 2.50e+03 pdb=" N ASP D 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 698 2.77 - 3.30: 3171 3.30 - 3.84: 5199 3.84 - 4.37: 4502 4.37 - 4.90: 7958 Nonbonded interactions: 21528 Sorted by model distance: nonbonded pdb=" O VAL B 132 " pdb=" N ASP B 136 " model vdw 2.240 3.120 nonbonded pdb=" O VAL A 132 " pdb=" N ASP A 136 " model vdw 2.240 3.120 nonbonded pdb=" O ASP A 13 " pdb=" N ARG A 67 " model vdw 2.416 3.120 nonbonded pdb=" O ASP B 13 " pdb=" N ARG B 67 " model vdw 2.416 3.120 nonbonded pdb=" N TYR D 12 " pdb=" O GLU D 65 " model vdw 2.422 3.120 ... (remaining 21523 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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: 5.410 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 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 : 0.001 0.009 3284 Z= 0.107 Angle : 0.417 4.868 4572 Z= 0.278 Chirality : 0.043 0.121 632 Planarity : 0.001 0.006 660 Dihedral : 3.804 13.288 660 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.23 (0.35), residues: 656 helix: 2.61 (0.28), residues: 360 sheet: -1.18 (0.63), residues: 80 loop : -1.61 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0448 time to fit residues: 0.2605 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 22.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.111259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105492 restraints weight = 33749.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105767 restraints weight = 27869.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.105804 restraints weight = 25019.161| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3284 Z= 0.431 Angle : 0.871 5.195 4572 Z= 0.596 Chirality : 0.048 0.126 632 Planarity : 0.007 0.024 660 Dihedral : 8.455 38.941 660 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 1.83 % Allowed : 8.54 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -2.31 (0.30), residues: 656 helix: -0.57 (0.25), residues: 388 sheet: -2.13 (0.51), residues: 80 loop : -3.10 (0.36), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0131 time to fit residues: 0.2040 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104444 restraints weight = 35310.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104947 restraints weight = 27197.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105173 restraints weight = 24586.247| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 1.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.360 Angle : 0.831 5.366 4572 Z= 0.560 Chirality : 0.047 0.122 632 Planarity : 0.006 0.032 660 Dihedral : 7.922 30.550 660 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.98 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.23 % 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: -2.74 (0.29), residues: 656 helix: -1.06 (0.24), residues: 376 sheet: -2.31 (0.62), residues: 72 loop : -2.81 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0128 time to fit residues: 0.1948 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.108403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102003 restraints weight = 34944.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102389 restraints weight = 28424.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102777 restraints weight = 26485.171| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 1.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.361 Angle : 0.819 5.562 4572 Z= 0.554 Chirality : 0.046 0.120 632 Planarity : 0.005 0.030 660 Dihedral : 8.057 33.399 660 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.24 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.13 (0.29), residues: 656 helix: -1.33 (0.23), residues: 384 sheet: -2.71 (0.60), residues: 72 loop : -3.02 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0122 time to fit residues: 0.1843 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.108092 restraints weight = 3399.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.108087 restraints weight = 4126.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.108086 restraints weight = 3890.020| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 1.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.322 Angle : 0.777 5.127 4572 Z= 0.525 Chirality : 0.046 0.118 632 Planarity : 0.005 0.031 660 Dihedral : 7.666 34.357 660 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -2.92 (0.30), residues: 656 helix: -1.14 (0.23), residues: 384 sheet: -2.78 (0.62), residues: 72 loop : -2.89 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0120 time to fit residues: 0.1863 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101074 restraints weight = 36496.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101957 restraints weight = 29143.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.102326 restraints weight = 26840.696| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 1.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.326 Angle : 0.783 5.210 4572 Z= 0.531 Chirality : 0.046 0.117 632 Planarity : 0.005 0.030 660 Dihedral : 7.821 34.434 660 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -2.82 (0.31), residues: 656 helix: -1.13 (0.24), residues: 384 sheet: -2.69 (0.65), residues: 72 loop : -2.72 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0134 time to fit residues: 0.2001 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 17.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.101760 restraints weight = 35074.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102691 restraints weight = 28449.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102890 restraints weight = 25635.979| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5339 moved from start: 1.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.323 Angle : 0.794 5.396 4572 Z= 0.537 Chirality : 0.046 0.116 632 Planarity : 0.005 0.030 660 Dihedral : 7.523 31.698 660 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.02 (0.29), residues: 656 helix: -1.15 (0.23), residues: 380 sheet: -3.21 (0.59), residues: 72 loop : -2.90 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0129 time to fit residues: 0.1961 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.107746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101180 restraints weight = 34572.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101875 restraints weight = 27052.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.101842 restraints weight = 26041.869| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 1.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 3284 Z= 0.299 Angle : 0.760 5.080 4572 Z= 0.514 Chirality : 0.045 0.116 632 Planarity : 0.005 0.030 660 Dihedral : 7.351 34.499 660 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 1.22 % Allowed : 15.24 % Favored : 83.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -2.82 (0.31), residues: 656 helix: -0.93 (0.25), residues: 380 sheet: -3.47 (0.58), residues: 72 loop : -2.80 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0127 time to fit residues: 0.1947 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101452 restraints weight = 34895.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101627 restraints weight = 28540.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101918 restraints weight = 25843.086| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 1.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.363 Angle : 0.834 5.727 4572 Z= 0.565 Chirality : 0.046 0.117 632 Planarity : 0.005 0.032 660 Dihedral : 7.935 33.498 660 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.68 % Favored : 81.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.34 (0.29), residues: 656 helix: -1.39 (0.23), residues: 380 sheet: -3.74 (0.58), residues: 72 loop : -2.89 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0131 time to fit residues: 0.1971 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 14.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101281 restraints weight = 35739.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101995 restraints weight = 30904.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102435 restraints weight = 26273.349| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 1.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.012 3284 Z= 0.276 Angle : 0.758 4.810 4572 Z= 0.511 Chirality : 0.045 0.116 632 Planarity : 0.005 0.030 660 Dihedral : 7.769 33.470 660 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.68 % Favored : 81.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.05 (0.30), residues: 656 helix: -1.12 (0.24), residues: 380 sheet: -3.84 (0.57), residues: 72 loop : -2.76 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0125 time to fit residues: 0.1860 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 30.0000 overall best weight: 16.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.107985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101070 restraints weight = 35793.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.102032 restraints weight = 29909.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102247 restraints weight = 26063.281| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 1.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 3284 Z= 0.301 Angle : 0.774 5.277 4572 Z= 0.523 Chirality : 0.045 0.115 632 Planarity : 0.005 0.030 660 Dihedral : 7.644 33.546 660 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 18.90 % Favored : 80.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.13 (0.30), residues: 656 helix: -1.21 (0.24), residues: 380 sheet: -3.90 (0.59), residues: 72 loop : -2.73 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 914.83 seconds wall clock time: 17 minutes 6.05 seconds (1026.05 seconds total)