Starting phenix.real_space_refine on Mon Sep 23 14:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/09_2024/7jlx_22383.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/09_2024/7jlx_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_22383/09_2024/7jlx_22383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/09_2024/7jlx_22383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/09_2024/7jlx_22383.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlx_22383/09_2024/7jlx_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-5461/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: 3.56, per 1000 atoms: 1.08 Number of scatterers: 3288 At special positions: 0 Unit cell: (95.7372, 93.86, 53.5002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 664 8.00 N 664 7.00 C 1960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 597.1 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: 0.47 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: 0.93 Time building geometry restraints manager: 1.14 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: 0.00 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: 4.460 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- 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 : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0449 time to fit residues: 0.2573 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 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0130 time to fit residues: 0.1955 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 moved from start: 1.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.360 Angle : 0.831 5.366 4572 Z= 0.560 Chirality : 0.047 0.122 632 Planarity : 0.006 0.032 660 Dihedral : 7.922 30.550 660 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.98 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.29), residues: 656 helix: -1.06 (0.24), residues: 376 sheet: -2.31 (0.62), residues: 72 loop : -2.81 (0.35), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0153 time to fit residues: 0.1934 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 1.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.361 Angle : 0.819 5.562 4572 Z= 0.554 Chirality : 0.046 0.120 632 Planarity : 0.005 0.030 660 Dihedral : 8.057 33.399 660 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.24 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.29), residues: 656 helix: -1.33 (0.23), residues: 384 sheet: -2.71 (0.60), residues: 72 loop : -3.02 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0122 time to fit residues: 0.1923 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4970 moved from start: 1.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.322 Angle : 0.777 5.127 4572 Z= 0.525 Chirality : 0.046 0.118 632 Planarity : 0.005 0.031 660 Dihedral : 7.666 34.357 660 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.30), residues: 656 helix: -1.14 (0.23), residues: 384 sheet: -2.78 (0.62), residues: 72 loop : -2.89 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. 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: 0.0120 time to fit residues: 0.1790 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 ------------------------------------------------------------------------------- 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: 20.0000 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: 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: 0.4985 moved from start: 1.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3284 Z= 0.363 Angle : 0.838 5.739 4572 Z= 0.568 Chirality : 0.046 0.121 632 Planarity : 0.005 0.031 660 Dihedral : 8.325 34.817 660 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 1.22 % Allowed : 17.68 % 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: -3.19 (0.30), residues: 656 helix: -1.36 (0.23), residues: 384 sheet: -2.88 (0.63), residues: 72 loop : -3.02 (0.40), 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 fitting. 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: 0.0121 time to fit residues: 0.1884 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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: 30.0000 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: 30.0000 chunk 36 optimal weight: 20.0000 chunk 18 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: 0.4996 moved from start: 1.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 3284 Z= 0.359 Angle : 0.834 5.735 4572 Z= 0.564 Chirality : 0.046 0.118 632 Planarity : 0.005 0.031 660 Dihedral : 7.988 35.636 660 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.85 % 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: -3.29 (0.29), residues: 656 helix: -1.36 (0.23), residues: 376 sheet: -3.36 (0.57), residues: 72 loop : -3.00 (0.37), 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 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 : 0.127 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0178 time to fit residues: 0.2588 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5013 moved from start: 1.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3284 Z= 0.396 Angle : 0.878 6.076 4572 Z= 0.594 Chirality : 0.047 0.122 632 Planarity : 0.006 0.032 660 Dihedral : 8.485 35.711 660 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 1.83 % Allowed : 17.07 % 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: -3.63 (0.29), residues: 656 helix: -1.67 (0.22), residues: 380 sheet: -3.78 (0.56), residues: 72 loop : -2.97 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP B 82 PHE 0.000 0.000 PHE B 15 TYR 0.000 0.000 TYR B 12 *********************** REFINEMENT MACRO_CYCLE 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 : 0.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0116 time to fit residues: 0.1744 Evaluate side-chains 2 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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: 0.2980 chunk 28 optimal weight: 0.8980 overall best weight: 10.2392 ------------------------------------------------------------------------------- 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: 0.4977 moved from start: 1.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 3284 Z= 0.215 Angle : 0.680 4.528 4572 Z= 0.457 Chirality : 0.044 0.115 632 Planarity : 0.004 0.028 660 Dihedral : 6.834 32.212 660 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.41 % Favored : 85.98 % 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: -2.41 (0.32), residues: 656 helix: -0.61 (0.25), residues: 380 sheet: -3.71 (0.57), residues: 72 loop : -2.44 (0.43), 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0125 time to fit residues: 0.1918 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 1.1161 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= 0.298 Angle : 0.759 5.105 4572 Z= 0.513 Chirality : 0.045 0.115 632 Planarity : 0.004 0.030 660 Dihedral : 7.487 35.248 660 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 1.22 % Allowed : 15.85 % 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: -2.79 (0.31), residues: 656 helix: -1.01 (0.24), residues: 404 sheet: -3.80 (0.57), residues: 72 loop : -2.55 (0.44), residues: 180 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 : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0123 time to fit residues: 0.1896 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 ------------------------------------------------------------------------------- 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: 30.0000 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098671 restraints weight = 35890.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098992 restraints weight = 29053.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.099139 restraints weight = 27489.053| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 moved from start: 1.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.015 3284 Z= 0.365 Angle : 0.822 5.063 4572 Z= 0.559 Chirality : 0.046 0.119 632 Planarity : 0.005 0.032 660 Dihedral : 8.029 34.860 660 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 1.22 % Allowed : 17.68 % 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: -3.30 (0.29), residues: 656 helix: -1.44 (0.22), residues: 404 sheet: -3.86 (0.59), residues: 72 loop : -2.73 (0.42), residues: 180 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: 890.49 seconds wall clock time: 16 minutes 36.34 seconds (996.34 seconds total)