Starting phenix.real_space_refine on Thu Dec 7 16:34:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo0_33332/12_2023/7xo0_33332.pdb" } resolution = 3.0 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= 0.004 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 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" 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: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 1.61, per 1000 atoms: 0.63 Number of scatterers: 2550 At special positions: 0 Unit cell: (92.22, 91.16, 33.92, 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 504 8.00 N 444 7.00 C 1602 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: 0.97 Conformation dependent library (CDL) restraints added in 515.6 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.605A pdb=" N VAL A 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER D 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.934A pdb=" N VAL C 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA A 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY D 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N HIS A 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA D 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N VAL A 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N VAL D 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 68 removed outlier: 6.156A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLY A 67 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 removed outlier: 6.310A pdb=" N VAL A 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.641A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.598A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.417A pdb=" N ILE A 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.512A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.589A pdb=" N VAL B 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL F 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER F 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 55 removed outlier: 6.940A pdb=" N VAL E 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR E 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY F 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N HIS B 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA F 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL B 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N VAL F 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N THR B 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 61 through 68 removed outlier: 6.157A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY F 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY B 67 " --> pdb=" O GLY F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 71 through 72 removed outlier: 6.306A pdb=" N VAL B 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.651A pdb=" N VAL B 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.628A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.425A pdb=" N ILE B 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.541A pdb=" N VAL B 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.63 Time building geometry restraints manager: 1.07 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: 438 1.29 - 1.35: 402 1.35 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA VAL F 70 " pdb=" CB VAL F 70 " ideal model delta sigma weight residual 1.533 1.540 -0.008 1.20e-02 6.94e+03 3.97e-01 bond pdb=" CA VAL D 70 " pdb=" CB VAL D 70 " ideal model delta sigma weight residual 1.533 1.540 -0.007 1.20e-02 6.94e+03 3.62e-01 bond pdb=" CA VAL C 70 " pdb=" CB VAL C 70 " ideal model delta sigma weight residual 1.533 1.539 -0.007 1.20e-02 6.94e+03 3.03e-01 bond pdb=" CA LYS E 43 " pdb=" C LYS E 43 " ideal model delta sigma weight residual 1.526 1.531 -0.006 1.08e-02 8.57e+03 2.80e-01 bond pdb=" CA VAL A 70 " pdb=" CB VAL A 70 " ideal model delta sigma weight residual 1.533 1.539 -0.006 1.20e-02 6.94e+03 2.71e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 106.11 - 111.13: 1117 111.13 - 116.15: 768 116.15 - 121.17: 738 121.17 - 126.19: 833 126.19 - 131.20: 6 Bond angle restraints: 3462 Sorted by residual: angle pdb=" N VAL C 74 " pdb=" CA VAL C 74 " pdb=" C VAL C 74 " ideal model delta sigma weight residual 112.35 110.49 1.86 1.41e+00 5.03e-01 1.74e+00 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.71e+00 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.35 110.51 1.84 1.41e+00 5.03e-01 1.70e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 1260 12.00 - 23.99: 108 23.99 - 35.98: 66 35.98 - 47.98: 18 47.98 - 59.97: 36 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CG LYS F 58 " pdb=" CD LYS F 58 " pdb=" CE LYS F 58 " pdb=" NZ LYS F 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 58 " pdb=" CD LYS B 58 " pdb=" CE LYS B 58 " pdb=" NZ LYS B 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.87 57.13 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS D 58 " pdb=" CD LYS D 58 " pdb=" CE LYS D 58 " pdb=" NZ LYS D 58 " ideal model delta sinusoidal sigma weight residual 180.00 122.88 57.12 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 236 0.025 - 0.050: 126 0.050 - 0.075: 12 0.075 - 0.100: 21 0.100 - 0.124: 61 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 73 " 0.002 2.00e-02 2.50e+03 4.16e-03 1.73e-01 pdb=" C GLY C 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY C 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL C 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 73 " 0.002 2.00e-02 2.50e+03 4.12e-03 1.70e-01 pdb=" C GLY D 73 " -0.007 2.00e-02 2.50e+03 pdb=" O GLY D 73 " 0.003 2.00e-02 2.50e+03 pdb=" N VAL D 74 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 73 " -0.002 2.00e-02 2.50e+03 4.11e-03 1.69e-01 pdb=" C GLY E 73 " 0.007 2.00e-02 2.50e+03 pdb=" O GLY E 73 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL E 74 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 536 2.80 - 3.33: 1921 3.33 - 3.85: 4042 3.85 - 4.38: 4053 4.38 - 4.90: 8187 Nonbonded interactions: 18739 Sorted by model distance: nonbonded pdb=" ND2 ASN A 65 " pdb=" OG1 THR C 92 " model vdw 2.280 2.520 nonbonded pdb=" OG1 THR A 92 " pdb=" ND2 ASN D 65 " model vdw 2.283 2.520 nonbonded pdb=" OG1 THR B 92 " pdb=" ND2 ASN F 65 " model vdw 2.283 2.520 nonbonded pdb=" ND2 ASN B 65 " pdb=" OG1 THR E 92 " model vdw 2.292 2.520 nonbonded pdb=" O ALA A 90 " pdb=" ND2 ASN D 65 " model vdw 2.301 2.520 ... (remaining 18734 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.010 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: 4.740 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.820 Find NCS groups from input model: 0.170 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 0.010 2562 Z= 0.096 Angle : 0.392 2.232 3462 Z= 0.243 Chirality : 0.050 0.124 456 Planarity : 0.001 0.004 426 Dihedral : 16.618 59.972 864 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.001 0.000 PHE E 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.229 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 1.5147 time to fit residues: 29.5592 Evaluate side-chains 15 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2562 Z= 0.132 Angle : 0.357 2.116 3462 Z= 0.216 Chirality : 0.051 0.123 456 Planarity : 0.001 0.005 426 Dihedral : 3.518 10.925 372 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.78 % Allowed : 14.34 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.001 0.001 PHE B 94 TYR 0.006 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.283 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 31 average time/residue: 1.5182 time to fit residues: 48.2055 Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2562 Z= 0.264 Angle : 0.426 2.409 3462 Z= 0.257 Chirality : 0.053 0.125 456 Planarity : 0.002 0.010 426 Dihedral : 3.887 13.932 372 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.10 % Allowed : 13.57 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE C 94 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.258 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 37 average time/residue: 1.3920 time to fit residues: 52.6479 Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2562 Z= 0.201 Angle : 0.409 4.624 3462 Z= 0.243 Chirality : 0.053 0.125 456 Planarity : 0.002 0.010 426 Dihedral : 3.800 12.845 372 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.10 % Allowed : 15.12 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.011 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.261 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 1.1890 time to fit residues: 41.5067 Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.4591 time to fit residues: 1.7653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2562 Z= 0.132 Angle : 0.369 3.599 3462 Z= 0.222 Chirality : 0.052 0.125 456 Planarity : 0.001 0.010 426 Dihedral : 3.639 11.514 372 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.71 % Allowed : 17.05 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.001 0.000 PHE C 94 TYR 0.007 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.270 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 1.1989 time to fit residues: 43.0515 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0258 time to fit residues: 0.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2562 Z= 0.281 Angle : 0.435 2.932 3462 Z= 0.260 Chirality : 0.053 0.128 456 Planarity : 0.002 0.012 426 Dihedral : 3.951 13.480 372 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.001 PHE C 94 TYR 0.010 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.282 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 1.1798 time to fit residues: 43.6264 Evaluate side-chains 37 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6759 time to fit residues: 1.7527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 0.0010 chunk 23 optimal weight: 4.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2562 Z= 0.151 Angle : 0.380 3.122 3462 Z= 0.229 Chirality : 0.052 0.126 456 Planarity : 0.001 0.010 426 Dihedral : 3.757 12.038 372 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.71 % Allowed : 17.44 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.281 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 1.2145 time to fit residues: 46.1263 Evaluate side-chains 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0262 time to fit residues: 0.3866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2562 Z= 0.175 Angle : 0.386 2.891 3462 Z= 0.232 Chirality : 0.052 0.127 456 Planarity : 0.001 0.013 426 Dihedral : 3.757 12.246 372 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.012 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.308 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 1.2355 time to fit residues: 46.8854 Evaluate side-chains 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0267 time to fit residues: 0.4163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2562 Z= 0.144 Angle : 0.375 2.777 3462 Z= 0.226 Chirality : 0.052 0.126 456 Planarity : 0.001 0.013 426 Dihedral : 3.686 11.781 372 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.71 % Allowed : 17.83 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.001 0.001 PHE C 94 TYR 0.013 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.281 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 1.2360 time to fit residues: 45.6723 Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0267 time to fit residues: 0.4307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.026 2562 Z= 0.470 Angle : 0.533 2.814 3462 Z= 0.316 Chirality : 0.057 0.131 456 Planarity : 0.003 0.015 426 Dihedral : 4.270 14.811 372 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 1.94 % Allowed : 18.60 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.002 PHE C 94 TYR 0.013 0.002 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.291 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 1.4637 time to fit residues: 59.8169 Evaluate side-chains 39 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.3742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.102905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092973 restraints weight = 3361.126| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.54 r_work: 0.3087 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 2562 Z= 0.176 Angle : 0.400 2.760 3462 Z= 0.240 Chirality : 0.053 0.126 456 Planarity : 0.002 0.014 426 Dihedral : 3.912 12.818 372 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.94 % Allowed : 18.60 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.002 0.001 PHE C 94 TYR 0.008 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.72 seconds wall clock time: 25 minutes 35.88 seconds (1535.88 seconds total)