Starting phenix.real_space_refine on Sun May 11 20:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.map" model { file = "/net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i65_52650/05_2025/9i65_52650.cif" } resolution = 4.1 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= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 5427 2.51 5 N 1305 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "L" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Time building chain proxies: 5.57, per 1000 atoms: 0.66 Number of scatterers: 8433 At special positions: 0 Unit cell: (63.9, 63.9, 315.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1692 8.00 N 1305 7.00 C 5427 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: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 27 sheets defined 3.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'G' and resid 84 through 88 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.520A pdb=" N LEU L 87 " --> pdb=" O GLN L 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 42 removed outlier: 4.116A pdb=" N MET M 41 " --> pdb=" O THR M 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE M 42 " --> pdb=" O ALA M 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 38 through 42' Processing helix chain 'M' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.520A pdb=" N THR E 133 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.865A pdb=" N VAL E 21 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 108 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 50 removed outlier: 4.172A pdb=" N THR E 47 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 49 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'F' and resid 17 through 18 removed outlier: 3.895A pdb=" N THR F 126 " --> pdb=" O THR F 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 54 through 56 removed outlier: 4.048A pdb=" N VAL F 108 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE F 37 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR F 106 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL F 76 " --> pdb=" O GLN F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 9 through 11 Processing sheet with id=AA9, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AB1, first strand: chain 'G' and resid 21 through 35 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 60 through 61 current: chain 'G' and resid 81 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 81 through 82 current: chain 'J' and resid 54 through 56 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 56 current: chain 'J' and resid 81 through 83 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 81 through 83 current: chain 'M' and resid 81 through 82 Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.521A pdb=" N THR H 133 " --> pdb=" O VAL H 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.841A pdb=" N VAL H 108 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 109 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL H 76 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.905A pdb=" N ILE H 49 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AB8, first strand: chain 'I' and resid 22 through 35 removed outlier: 4.099A pdb=" N VAL I 108 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL I 76 " --> pdb=" O GLN I 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AC1, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.824A pdb=" N THR J 126 " --> pdb=" O THR J 18 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.550A pdb=" N VAL K 11 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 60 through 61 removed outlier: 7.346A pdb=" N VAL K 21 " --> pdb=" O THR K 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 122 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL K 108 " --> pdb=" O ALA K 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.734A pdb=" N ILE K 49 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.505A pdb=" N VAL L 11 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 133 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.721A pdb=" N VAL L 21 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL L 108 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE L 37 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR L 106 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 76 " --> pdb=" O GLN L 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 48 through 50 removed outlier: 3.638A pdb=" N ILE L 49 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 9 through 12 212 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2691 1.34 - 1.46: 1658 1.46 - 1.57: 4228 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8595 Sorted by residual: bond pdb=" CA ILE L 49 " pdb=" CB ILE L 49 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.23e-02 6.61e+03 2.42e+00 bond pdb=" CA ALA K 51 " pdb=" C ALA K 51 " ideal model delta sigma weight residual 1.522 1.501 0.020 1.72e-02 3.38e+03 1.39e+00 bond pdb=" N ILE L 37 " pdb=" CA ILE L 37 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.04e+00 bond pdb=" N GLY G 80 " pdb=" CA GLY G 80 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.03e+00 bond pdb=" C GLY F 44 " pdb=" N GLY F 45 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.51e-01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11529 1.80 - 3.60: 329 3.60 - 5.40: 26 5.40 - 7.19: 4 7.19 - 8.99: 1 Bond angle restraints: 11889 Sorted by residual: angle pdb=" N ILE L 37 " pdb=" CA ILE L 37 " pdb=" C ILE L 37 " ideal model delta sigma weight residual 106.21 111.79 -5.58 1.07e+00 8.73e-01 2.72e+01 angle pdb=" C ASP E 57 " pdb=" N ALA E 58 " pdb=" CA ALA E 58 " ideal model delta sigma weight residual 121.90 116.87 5.03 1.26e+00 6.30e-01 1.59e+01 angle pdb=" N VAL H 93 " pdb=" CA VAL H 93 " pdb=" C VAL H 93 " ideal model delta sigma weight residual 113.53 109.79 3.74 9.80e-01 1.04e+00 1.45e+01 angle pdb=" C VAL I 3 " pdb=" N ILE I 4 " pdb=" CA ILE I 4 " ideal model delta sigma weight residual 121.97 127.73 -5.76 1.80e+00 3.09e-01 1.02e+01 angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 113.53 110.63 2.90 9.80e-01 1.04e+00 8.73e+00 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4695 16.11 - 32.23: 302 32.23 - 48.34: 60 48.34 - 64.46: 4 64.46 - 80.57: 6 Dihedral angle restraints: 5067 sinusoidal: 1629 harmonic: 3438 Sorted by residual: dihedral pdb=" CA GLU L 104 " pdb=" C GLU L 104 " pdb=" N GLY L 105 " pdb=" CA GLY L 105 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR I 48 " pdb=" C THR I 48 " pdb=" N ILE I 49 " pdb=" CA ILE I 49 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA F 52 " pdb=" C ALA F 52 " pdb=" N SER F 53 " pdb=" CA SER F 53 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1299 0.058 - 0.116: 263 0.116 - 0.174: 29 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CB ILE L 37 " pdb=" CA ILE L 37 " pdb=" CG1 ILE L 37 " pdb=" CG2 ILE L 37 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE E 49 " pdb=" CA ILE E 49 " pdb=" CG1 ILE E 49 " pdb=" CG2 ILE E 49 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL J 108 " pdb=" N VAL J 108 " pdb=" C VAL J 108 " pdb=" CB VAL J 108 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1590 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 49 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.88e+00 pdb=" N PRO G 50 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 50 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 50 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 49 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO F 50 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 101 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C ASP I 101 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP I 101 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE I 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 410 2.71 - 3.26: 8515 3.26 - 3.80: 13037 3.80 - 4.35: 14900 4.35 - 4.90: 26185 Nonbonded interactions: 63047 Sorted by model distance: nonbonded pdb=" OG1 THR G 29 " pdb=" OG1 THR G 114 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR M 29 " pdb=" OG1 THR M 114 " model vdw 2.171 3.040 nonbonded pdb=" O VAL F 103 " pdb=" OG1 THR F 106 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR G 25 " pdb=" OD1 ASP G 118 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR H 29 " pdb=" OG1 THR H 114 " model vdw 2.186 3.040 ... (remaining 63042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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 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: 1.550 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.003 0.037 8595 Z= 0.154 Angle : 0.656 8.993 11889 Z= 0.363 Chirality : 0.047 0.290 1593 Planarity : 0.005 0.055 1503 Dihedral : 11.378 80.571 2871 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.28 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -1.25 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.21 (0.22), residues: 567 loop : -3.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE I 54 TYR 0.010 0.001 TYR F 34 ARG 0.003 0.000 ARG L 32 Details of bonding type rmsd hydrogen bonds : bond 0.30744 ( 212) hydrogen bonds : angle 13.38678 ( 525) covalent geometry : bond 0.00326 ( 8595) covalent geometry : angle 0.65602 (11889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 22 ILE cc_start: 0.9057 (mt) cc_final: 0.8803 (tt) REVERT: G 22 ILE cc_start: 0.8532 (mp) cc_final: 0.7991 (tt) REVERT: G 104 GLU cc_start: 0.7984 (pm20) cc_final: 0.7738 (pm20) REVERT: H 56 ASP cc_start: 0.6365 (t0) cc_final: 0.6146 (m-30) REVERT: I 83 GLN cc_start: 0.8079 (mt0) cc_final: 0.7814 (mt0) REVERT: I 106 THR cc_start: 0.8895 (m) cc_final: 0.8652 (p) REVERT: L 16 VAL cc_start: 0.8275 (t) cc_final: 0.8043 (m) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1276 time to fit residues: 29.6544 Evaluate side-chains 84 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 59 optimal weight: 0.0050 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 ASN ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150083 restraints weight = 14148.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148258 restraints weight = 21211.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148762 restraints weight = 22958.887| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8595 Z= 0.147 Angle : 0.664 11.817 11889 Z= 0.335 Chirality : 0.049 0.191 1593 Planarity : 0.005 0.048 1503 Dihedral : 5.148 37.365 1260 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.86 % Favored : 88.64 % Rotamer: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % 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: -0.94 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.41 (0.23), residues: 504 loop : -2.40 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE L 102 TYR 0.009 0.001 TYR F 73 ARG 0.003 0.001 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 212) hydrogen bonds : angle 8.03169 ( 525) covalent geometry : bond 0.00337 ( 8595) covalent geometry : angle 0.66372 (11889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.924 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1265 time to fit residues: 20.3065 Evaluate side-chains 73 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.161547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146418 restraints weight = 14496.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145250 restraints weight = 22421.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145384 restraints weight = 25405.154| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8595 Z= 0.163 Angle : 0.669 12.914 11889 Z= 0.335 Chirality : 0.049 0.182 1593 Planarity : 0.005 0.057 1503 Dihedral : 5.251 40.128 1260 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.70 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: -1.05 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.25 (0.23), residues: 504 loop : -2.41 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE I 54 TYR 0.014 0.001 TYR K 34 ARG 0.002 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 212) hydrogen bonds : angle 7.01551 ( 525) covalent geometry : bond 0.00399 ( 8595) covalent geometry : angle 0.66920 (11889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: J 4 ILE cc_start: 0.6659 (mp) cc_final: 0.6375 (mm) REVERT: M 49 ILE cc_start: 0.3454 (pt) cc_final: 0.3223 (pt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1254 time to fit residues: 17.7931 Evaluate side-chains 76 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.161495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.146695 restraints weight = 14332.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145172 restraints weight = 22115.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140694 restraints weight = 25377.851| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8595 Z= 0.164 Angle : 0.672 10.508 11889 Z= 0.336 Chirality : 0.049 0.196 1593 Planarity : 0.005 0.049 1503 Dihedral : 5.300 43.273 1260 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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: -1.10 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.10 (0.23), residues: 504 loop : -2.33 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE I 54 TYR 0.010 0.001 TYR F 73 ARG 0.003 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 212) hydrogen bonds : angle 6.65447 ( 525) covalent geometry : bond 0.00401 ( 8595) covalent geometry : angle 0.67209 (11889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: J 4 ILE cc_start: 0.6646 (mp) cc_final: 0.6392 (mm) REVERT: L 83 GLN cc_start: 0.8025 (mm110) cc_final: 0.7714 (mm-40) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1283 time to fit residues: 17.7021 Evaluate side-chains 74 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 0.0470 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 overall best weight: 0.3894 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.148342 restraints weight = 14150.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.146965 restraints weight = 22255.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.146415 restraints weight = 24783.521| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8595 Z= 0.120 Angle : 0.637 12.830 11889 Z= 0.316 Chirality : 0.048 0.140 1593 Planarity : 0.004 0.046 1503 Dihedral : 5.077 45.199 1260 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.61 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -0.88 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.21 (0.23), residues: 504 loop : -2.15 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE I 54 TYR 0.023 0.001 TYR K 34 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 212) hydrogen bonds : angle 6.09612 ( 525) covalent geometry : bond 0.00295 ( 8595) covalent geometry : angle 0.63683 (11889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: H 41 MET cc_start: 0.2602 (ttp) cc_final: 0.2297 (tmm) REVERT: J 4 ILE cc_start: 0.6580 (mp) cc_final: 0.6273 (mm) REVERT: L 82 LEU cc_start: 0.7961 (mt) cc_final: 0.7568 (tt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1348 time to fit residues: 18.5823 Evaluate side-chains 72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 51 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.163328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144421 restraints weight = 14314.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.143032 restraints weight = 14699.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142761 restraints weight = 16702.703| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8595 Z= 0.142 Angle : 0.662 14.253 11889 Z= 0.326 Chirality : 0.048 0.220 1593 Planarity : 0.004 0.046 1503 Dihedral : 5.109 46.108 1260 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.11 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -0.88 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.18 (0.23), residues: 504 loop : -2.12 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE F 54 TYR 0.011 0.001 TYR L 73 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 212) hydrogen bonds : angle 6.00804 ( 525) covalent geometry : bond 0.00350 ( 8595) covalent geometry : angle 0.66221 (11889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.884 Fit side-chains REVERT: J 4 ILE cc_start: 0.6576 (mp) cc_final: 0.6327 (mm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1340 time to fit residues: 17.6689 Evaluate side-chains 72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.0010 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.165279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.151033 restraints weight = 14238.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.149696 restraints weight = 22442.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.148996 restraints weight = 25022.316| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8595 Z= 0.124 Angle : 0.654 11.942 11889 Z= 0.323 Chirality : 0.048 0.173 1593 Planarity : 0.004 0.046 1503 Dihedral : 5.053 46.919 1260 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.95 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -0.78 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.22 (0.23), residues: 504 loop : -2.03 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE I 54 TYR 0.023 0.001 TYR K 34 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 212) hydrogen bonds : angle 5.80438 ( 525) covalent geometry : bond 0.00307 ( 8595) covalent geometry : angle 0.65440 (11889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.859 Fit side-chains REVERT: J 4 ILE cc_start: 0.6566 (mp) cc_final: 0.6243 (mm) REVERT: M 41 MET cc_start: 0.0714 (ptm) cc_final: 0.0511 (ptm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1273 time to fit residues: 17.9400 Evaluate side-chains 69 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.161873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145734 restraints weight = 14201.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.143606 restraints weight = 24684.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143873 restraints weight = 26759.164| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8595 Z= 0.171 Angle : 0.694 10.856 11889 Z= 0.345 Chirality : 0.049 0.202 1593 Planarity : 0.004 0.046 1503 Dihedral : 5.284 47.471 1260 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.53 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.91 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.08 (0.22), residues: 504 loop : -2.06 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE L 54 TYR 0.012 0.001 TYR L 73 ARG 0.002 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 212) hydrogen bonds : angle 6.09499 ( 525) covalent geometry : bond 0.00420 ( 8595) covalent geometry : angle 0.69393 (11889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: J 4 ILE cc_start: 0.6581 (mp) cc_final: 0.6274 (mm) REVERT: L 83 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7999 (mm-40) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1338 time to fit residues: 17.1453 Evaluate side-chains 63 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.164033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150591 restraints weight = 14416.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148807 restraints weight = 23923.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.149099 restraints weight = 24636.781| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8595 Z= 0.157 Angle : 0.689 10.675 11889 Z= 0.344 Chirality : 0.049 0.165 1593 Planarity : 0.004 0.046 1503 Dihedral : 5.307 48.916 1260 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.45 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.90 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.07 (0.22), residues: 504 loop : -2.05 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE H 54 TYR 0.027 0.002 TYR K 34 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 212) hydrogen bonds : angle 5.91780 ( 525) covalent geometry : bond 0.00384 ( 8595) covalent geometry : angle 0.68861 (11889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.881 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1293 time to fit residues: 16.2527 Evaluate side-chains 61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.161631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142029 restraints weight = 14325.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.140277 restraints weight = 15357.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139982 restraints weight = 18556.362| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8595 Z= 0.187 Angle : 0.715 10.817 11889 Z= 0.356 Chirality : 0.049 0.180 1593 Planarity : 0.005 0.049 1503 Dihedral : 5.434 49.554 1260 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.70 % Favored : 86.88 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.02 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.96 (0.22), residues: 504 loop : -2.10 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE G 54 TYR 0.015 0.001 TYR L 73 ARG 0.002 0.000 ARG F 32 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 212) hydrogen bonds : angle 6.11022 ( 525) covalent geometry : bond 0.00455 ( 8595) covalent geometry : angle 0.71514 (11889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.855 Fit side-chains REVERT: G 79 ASN cc_start: 0.8251 (t0) cc_final: 0.7636 (t0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1218 time to fit residues: 15.0368 Evaluate side-chains 61 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146534 restraints weight = 14285.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144631 restraints weight = 23582.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.144548 restraints weight = 26005.991| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8595 Z= 0.173 Angle : 0.695 9.747 11889 Z= 0.348 Chirality : 0.049 0.164 1593 Planarity : 0.005 0.049 1503 Dihedral : 5.417 50.405 1260 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.36 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.06 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.89 (0.22), residues: 504 loop : -2.09 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE F 54 TYR 0.028 0.002 TYR K 34 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 212) hydrogen bonds : angle 6.08419 ( 525) covalent geometry : bond 0.00426 ( 8595) covalent geometry : angle 0.69538 (11889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.10 seconds wall clock time: 40 minutes 34.37 seconds (2434.37 seconds total)