Starting phenix.real_space_refine on Thu Dec 7 17:53:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_22383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_22383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_22383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_22383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/12_2023/7jlx_22383.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3288 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" 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: "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 Chain: "D" 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 Time building chain proxies: 2.45, per 1000 atoms: 0.75 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 - 3.50 Amino acid : False - 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: 1.43 Conformation dependent library (CDL) restraints added in 935.2 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: 0.48 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: 1.02 Time building geometry restraints manager: 1.53 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: 102.85 - 107.56: 11 107.56 - 112.27: 1777 112.27 - 116.98: 377 116.98 - 121.70: 1533 121.70 - 126.41: 874 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 2.520 nonbonded pdb=" O VAL A 132 " pdb=" N ASP A 136 " model vdw 2.240 2.520 nonbonded pdb=" O ASP A 13 " pdb=" N ARG A 67 " model vdw 2.416 2.520 nonbonded pdb=" O ASP B 13 " pdb=" N ARG B 67 " model vdw 2.416 2.520 nonbonded pdb=" N TYR D 12 " pdb=" O GLU D 65 " model vdw 2.422 2.520 ... (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 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: 5.950 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: 0.000 Extract box with map and model: 22.670 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.520 ------------------------------------------------------------------------------- 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 fitting. 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: 0.0445 time to fit residues: 0.2622 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1284 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 58 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4939 moved from start: 1.0252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3284 Z= 0.388 Angle : 0.844 6.026 4572 Z= 0.573 Chirality : 0.048 0.125 632 Planarity : 0.006 0.023 660 Dihedral : 8.345 38.807 660 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 2.44 % Allowed : 8.54 % Favored : 89.02 % 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: -2.13 (0.30), residues: 656 helix: -0.41 (0.26), residues: 388 sheet: -2.01 (0.51), residues: 80 loop : -3.09 (0.37), 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 fitting. 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: 0.0125 time to fit residues: 0.1938 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1267 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 1.0397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3284 Z= 0.330 Angle : 0.780 4.484 4572 Z= 0.528 Chirality : 0.046 0.122 632 Planarity : 0.005 0.033 660 Dihedral : 8.492 47.054 660 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % 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: -2.53 (0.31), residues: 656 helix: -0.70 (0.26), residues: 364 sheet: -1.97 (0.66), residues: 72 loop : -3.15 (0.34), residues: 220 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0128 time to fit residues: 0.1964 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1258 ------------------------------------------------------------------------------- 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: 40.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 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: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4956 moved from start: 1.0638 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= 0.365 Angle : 0.809 5.108 4572 Z= 0.550 Chirality : 0.046 0.119 632 Planarity : 0.006 0.030 660 Dihedral : 8.517 45.493 660 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.90 % Favored : 81.10 % 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: -3.11 (0.30), residues: 656 helix: -1.19 (0.24), residues: 372 sheet: -2.42 (0.65), residues: 72 loop : -3.33 (0.35), residues: 212 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 fitting. 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: 0.0139 time to fit residues: 0.2030 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1387 ------------------------------------------------------------------------------- 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: 30.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 overall best weight: 16.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4946 moved from start: 1.0601 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 : 0.747 4.729 4572 Z= 0.505 Chirality : 0.045 0.117 632 Planarity : 0.005 0.027 660 Dihedral : 8.094 44.621 660 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.29 % 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: -2.97 (0.30), residues: 656 helix: -1.02 (0.25), residues: 372 sheet: -2.69 (0.64), residues: 72 loop : -3.26 (0.37), residues: 212 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 fitting. 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: 0.0127 time to fit residues: 0.1973 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1293 ------------------------------------------------------------------------------- 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: 0.8980 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 28 optimal weight: 0.0010 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 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: 10.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 moved from start: 1.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 3284 Z= 0.202 Angle : 0.658 3.750 4572 Z= 0.443 Chirality : 0.044 0.119 632 Planarity : 0.004 0.027 660 Dihedral : 7.537 43.377 660 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % 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: -2.34 (0.33), residues: 656 helix: -0.44 (0.27), residues: 372 sheet: -2.63 (0.65), residues: 72 loop : -3.05 (0.40), residues: 212 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 fitting. 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: 0.0123 time to fit residues: 0.1980 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1332 ------------------------------------------------------------------------------- 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: 40.0000 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 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: 20.0000 chunk 36 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 1.0709 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= 0.323 Angle : 0.771 4.549 4572 Z= 0.524 Chirality : 0.045 0.116 632 Planarity : 0.005 0.028 660 Dihedral : 8.188 43.470 660 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.34 % Favored : 78.66 % 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: -2.93 (0.31), residues: 656 helix: -1.06 (0.25), residues: 372 sheet: -2.62 (0.67), residues: 72 loop : -3.10 (0.40), residues: 212 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 fitting. 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: 0.0123 time to fit residues: 0.1935 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1254 ------------------------------------------------------------------------------- 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: 20.0000 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: 20.0000 chunk 59 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 chunk 57 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 1.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 3284 Z= 0.363 Angle : 0.825 5.240 4572 Z= 0.558 Chirality : 0.046 0.121 632 Planarity : 0.005 0.026 660 Dihedral : 8.445 45.817 660 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.46 % Favored : 82.93 % 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: -3.39 (0.29), residues: 656 helix: -1.43 (0.23), residues: 376 sheet: -2.97 (0.63), residues: 72 loop : -3.26 (0.36), 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 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0122 time to fit residues: 0.1879 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1247 ------------------------------------------------------------------------------- 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: 20.0000 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 28 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4978 moved from start: 1.1093 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= 0.326 Angle : 0.773 4.727 4572 Z= 0.524 Chirality : 0.045 0.115 632 Planarity : 0.005 0.027 660 Dihedral : 7.928 43.359 660 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % 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: -3.24 (0.30), residues: 656 helix: -1.30 (0.24), residues: 372 sheet: -3.07 (0.62), residues: 72 loop : -3.12 (0.38), residues: 212 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 fitting. 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: 0.0131 time to fit residues: 0.2064 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1255 ------------------------------------------------------------------------------- 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: 9.9990 chunk 58 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 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: 30.0000 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 overall best weight: 11.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 1.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 3284 Z= 0.227 Angle : 0.667 3.847 4572 Z= 0.450 Chirality : 0.044 0.115 632 Planarity : 0.004 0.026 660 Dihedral : 7.388 41.889 660 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % 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: -2.54 (0.33), residues: 656 helix: -0.51 (0.27), residues: 372 sheet: -3.38 (0.57), residues: 72 loop : -3.06 (0.40), residues: 212 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0137 time to fit residues: 0.2123 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1208 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 44 optimal weight: 0.0020 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 overall best weight: 10.0002 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.109909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.103326 restraints weight = 34987.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104101 restraints weight = 27402.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105081 restraints weight = 24201.250| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5281 moved from start: 1.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 3284 Z= 0.207 Angle : 0.653 3.888 4572 Z= 0.440 Chirality : 0.043 0.115 632 Planarity : 0.004 0.027 660 Dihedral : 7.172 41.054 660 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % 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: -2.25 (0.33), residues: 656 helix: -0.26 (0.27), residues: 372 sheet: -3.36 (0.57), residues: 72 loop : -2.92 (0.41), residues: 212 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: 959.51 seconds wall clock time: 17 minutes 54.52 seconds (1074.52 seconds total)