Starting phenix.real_space_refine on Wed Mar 5 18:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlx_22383/03_2025/7jlx_22383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlx_22383/03_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_22383/03_2025/7jlx_22383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlx_22383/03_2025/7jlx_22383.map" model { file = "/net/cci-nas-00/data/ceres_data/7jlx_22383/03_2025/7jlx_22383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlx_22383/03_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-5624/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: 3.50, per 1000 atoms: 1.06 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: 0.89 Conformation dependent library (CDL) restraints added in 579.2 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: 0.43 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: 0.80 Time building geometry restraints manager: 1.03 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: 4.590 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- 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 : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0399 time to fit residues: 0.2401 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 : 0.096 ------------------------------------------------------------------------------- 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 = 0.105488 restraints weight = 33749.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105762 restraints weight = 27849.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.105807 restraints weight = 25019.711| |-----------------------------------------------------------------------------| 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 : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0126 time to fit residues: 0.1934 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 : 0.097 ------------------------------------------------------------------------------- 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: 9.9990 chunk 46 optimal weight: 20.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- 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 = 0.110929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104653 restraints weight = 35200.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105094 restraints weight = 26884.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105455 restraints weight = 23613.815| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 1.0342 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= 0.327 Angle : 0.791 5.106 4572 Z= 0.533 Chirality : 0.046 0.122 632 Planarity : 0.005 0.032 660 Dihedral : 7.507 29.950 660 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.20 % Favored : 87.20 % 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: -2.45 (0.30), residues: 656 helix: -0.73 (0.25), residues: 368 sheet: -2.19 (0.63), residues: 72 loop : -2.84 (0.34), 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 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 : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0131 time to fit residues: 0.2016 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 : 0.090 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 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: 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 = 0.3793 r_free = 0.3793 target = 0.110260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.103989 restraints weight = 34578.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104433 restraints weight = 27739.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104755 restraints weight = 24237.223| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 moved from start: 1.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 3284 Z= 0.330 Angle : 0.776 4.995 4572 Z= 0.526 Chirality : 0.046 0.119 632 Planarity : 0.005 0.031 660 Dihedral : 7.701 33.839 660 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.02 % Favored : 85.37 % 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: -2.80 (0.29), residues: 656 helix: -1.01 (0.24), residues: 384 sheet: -2.54 (0.60), residues: 72 loop : -3.03 (0.36), 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 : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0115 time to fit residues: 0.1821 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 ------------------------------------------------------------------------------- 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: 0.0170 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 overall best weight: 14.0034 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.109839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103123 restraints weight = 35897.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103892 restraints weight = 29309.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104074 restraints weight = 25477.768| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 1.0492 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= 0.265 Angle : 0.709 4.443 4572 Z= 0.479 Chirality : 0.045 0.116 632 Planarity : 0.004 0.029 660 Dihedral : 6.922 32.826 660 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.80 % Favored : 86.59 % 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: -2.39 (0.31), residues: 656 helix: -0.64 (0.25), residues: 384 sheet: -2.60 (0.62), residues: 72 loop : -2.87 (0.37), 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 : 0.106 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0126 time to fit residues: 0.1970 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 59 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- 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 = 0.108275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.101270 restraints weight = 34888.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101946 restraints weight = 28404.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102146 restraints weight = 25522.106| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5354 moved from start: 1.0670 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= 0.325 Angle : 0.779 4.950 4572 Z= 0.529 Chirality : 0.046 0.119 632 Planarity : 0.005 0.029 660 Dihedral : 7.737 33.693 660 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.44 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: -2.73 (0.30), residues: 656 helix: -1.01 (0.24), residues: 384 sheet: -2.69 (0.64), residues: 72 loop : -2.80 (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 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 : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0134 time to fit residues: 0.1834 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 : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 overall best weight: 15.7996 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.108368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101568 restraints weight = 34533.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.101977 restraints weight = 28313.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102561 restraints weight = 26761.515| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 1.0654 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= 0.290 Angle : 0.748 4.807 4572 Z= 0.506 Chirality : 0.045 0.116 632 Planarity : 0.005 0.031 660 Dihedral : 7.430 32.360 660 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.17 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: -2.69 (0.31), residues: 656 helix: -0.94 (0.24), residues: 384 sheet: -2.76 (0.65), residues: 72 loop : -2.83 (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 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 : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0136 time to fit residues: 0.2077 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 12 optimal weight: 30.0000 chunk 11 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 59 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 57 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 = 0.3767 r_free = 0.3767 target = 0.108949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102894 restraints weight = 34940.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102860 restraints weight = 29729.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103244 restraints weight = 26080.084| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 1.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 3284 Z= 0.399 Angle : 0.891 5.868 4572 Z= 0.606 Chirality : 0.047 0.124 632 Planarity : 0.006 0.033 660 Dihedral : 8.760 35.141 660 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 20.12 % Favored : 79.27 % 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: -3.65 (0.28), residues: 656 helix: -1.68 (0.22), residues: 384 sheet: -3.44 (0.58), residues: 72 loop : -3.17 (0.36), 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 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 : 0.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0144 time to fit residues: 0.1873 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 28 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 = 0.3760 r_free = 0.3760 target = 0.107870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101012 restraints weight = 35882.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101954 restraints weight = 30014.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102312 restraints weight = 26245.301| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 moved from start: 1.1066 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= 0.329 Angle : 0.798 5.584 4572 Z= 0.539 Chirality : 0.045 0.116 632 Planarity : 0.005 0.030 660 Dihedral : 7.642 34.416 660 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.63 % Favored : 84.76 % 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: -3.30 (0.29), residues: 656 helix: -1.33 (0.23), residues: 380 sheet: -3.54 (0.59), residues: 72 loop : -3.03 (0.37), 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 : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0116 time to fit residues: 0.1794 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 : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 overall best weight: 15.9998 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.108207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101224 restraints weight = 35681.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101566 restraints weight = 30087.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101761 restraints weight = 27708.155| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 1.1109 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= 0.299 Angle : 0.756 5.236 4572 Z= 0.511 Chirality : 0.045 0.114 632 Planarity : 0.005 0.030 660 Dihedral : 7.357 33.514 660 Min Nonbonded Distance : 2.246 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: -3.00 (0.30), residues: 656 helix: -1.05 (0.24), residues: 380 sheet: -3.72 (0.56), residues: 72 loop : -2.87 (0.37), 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 : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0122 time to fit residues: 0.1854 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 58 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 = 0.3710 r_free = 0.3710 target = 0.105741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098994 restraints weight = 33936.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099573 restraints weight = 29576.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100292 restraints weight = 25373.051| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 1.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.014 3284 Z= 0.333 Angle : 0.798 5.670 4572 Z= 0.540 Chirality : 0.046 0.115 632 Planarity : 0.005 0.031 660 Dihedral : 7.706 33.954 660 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.61 % Allowed : 19.51 % Favored : 79.88 % 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: -3.08 (0.30), residues: 656 helix: -1.22 (0.24), residues: 380 sheet: -3.84 (0.57), residues: 72 loop : -2.62 (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: 1018.49 seconds wall clock time: 18 minutes 20.21 seconds (1100.21 seconds total)