Starting phenix.real_space_refine on Wed Sep 17 11:29:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i65_52650/09_2025/9i65_52650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i65_52650/09_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_52650/09_2025/9i65_52650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i65_52650/09_2025/9i65_52650.map" model { file = "/net/cci-nas-00/data/ceres_data/9i65_52650/09_2025/9i65_52650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i65_52650/09_2025/9i65_52650.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.86, per 1000 atoms: 0.22 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: 0.71 Conformation dependent library (CDL) restraints added in 487.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 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: 1.19 Time building geometry restraints manager: 0.97 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: 0.00 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.610 Find NCS groups from input model: 0.140 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG L 32 TYR 0.010 0.001 TYR F 34 PHE 0.009 0.001 PHE I 54 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8595) covalent geometry : angle 0.65602 (11889) hydrogen bonds : bond 0.30744 ( 212) hydrogen bonds : angle 13.38678 ( 525) *********************** 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 : 0.307 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: 0.7990 (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: 0.7819 (mt0) REVERT: I 106 THR cc_start: 0.8895 (m) cc_final: 0.8648 (p) REVERT: L 16 VAL cc_start: 0.8275 (t) cc_final: 0.8042 (m) REVERT: L 83 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7571 (mm110) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0601 time to fit residues: 14.4145 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 M 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.162466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141739 restraints weight = 14485.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141500 restraints weight = 15137.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141499 restraints weight = 15735.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141498 restraints weight = 15735.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141498 restraints weight = 15740.071| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1716 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= 0.175 Angle : 0.690 10.758 11889 Z= 0.349 Chirality : 0.050 0.207 1593 Planarity : 0.005 0.049 1503 Dihedral : 5.298 37.185 1260 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.45 % Favored : 88.05 % Rotamer: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.30 (0.23), residues: 504 loop : -2.50 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 32 TYR 0.011 0.001 TYR F 73 PHE 0.013 0.001 PHE G 54 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8595) covalent geometry : angle 0.68981 (11889) hydrogen bonds : bond 0.04956 ( 212) hydrogen bonds : angle 8.25431 ( 525) *********************** 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 96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: F 22 ILE cc_start: 0.9474 (mt) cc_final: 0.9189 (tt) REVERT: I 106 THR cc_start: 0.8970 (m) cc_final: 0.8732 (p) REVERT: J 124 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8329 (mt0) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.0582 time to fit residues: 9.1636 Evaluate side-chains 73 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.0010 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137675 restraints weight = 14547.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137674 restraints weight = 15304.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137674 restraints weight = 15305.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137674 restraints weight = 15305.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137674 restraints weight = 15305.907| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8595 Z= 0.192 Angle : 0.700 11.961 11889 Z= 0.350 Chirality : 0.049 0.231 1593 Planarity : 0.005 0.059 1503 Dihedral : 5.565 41.335 1260 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.70 % Favored : 86.88 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.11 (0.23), residues: 504 loop : -2.54 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 32 TYR 0.019 0.002 TYR L 73 PHE 0.016 0.002 PHE I 54 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8595) covalent geometry : angle 0.70035 (11889) hydrogen bonds : bond 0.04462 ( 212) hydrogen bonds : angle 7.23810 ( 525) *********************** 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 92 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: F 41 MET cc_start: 0.5678 (pmm) cc_final: 0.3838 (ptp) REVERT: I 106 THR cc_start: 0.9032 (m) cc_final: 0.8766 (p) REVERT: I 124 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8607 (mm110) REVERT: J 4 ILE cc_start: 0.6606 (mp) cc_final: 0.6396 (mm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0574 time to fit residues: 8.7220 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 : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 88 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 0.0060 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.159830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137675 restraints weight = 14688.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137278 restraints weight = 16328.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137278 restraints weight = 16795.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137278 restraints weight = 16795.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137278 restraints weight = 16795.243| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8595 Z= 0.172 Angle : 0.692 10.082 11889 Z= 0.345 Chirality : 0.049 0.196 1593 Planarity : 0.005 0.049 1503 Dihedral : 5.504 44.887 1260 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.96 (0.22), residues: 504 loop : -2.43 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 32 TYR 0.023 0.002 TYR K 34 PHE 0.013 0.001 PHE I 54 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8595) covalent geometry : angle 0.69230 (11889) hydrogen bonds : bond 0.03795 ( 212) hydrogen bonds : angle 6.76355 ( 525) *********************** 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 87 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: I 106 THR cc_start: 0.8911 (m) cc_final: 0.8672 (p) REVERT: J 4 ILE cc_start: 0.6591 (mp) cc_final: 0.6360 (mm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0533 time to fit residues: 7.7969 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 64 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4540 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.163257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.148892 restraints weight = 14329.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.147217 restraints weight = 22556.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147538 restraints weight = 25474.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.147340 restraints weight = 20488.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.147340 restraints weight = 20327.520| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3093 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= 0.130 Angle : 0.656 12.293 11889 Z= 0.324 Chirality : 0.048 0.151 1593 Planarity : 0.005 0.046 1503 Dihedral : 5.264 46.878 1260 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.78 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.04 (0.22), residues: 504 loop : -2.26 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.010 0.001 TYR L 73 PHE 0.015 0.001 PHE I 54 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8595) covalent geometry : angle 0.65601 (11889) hydrogen bonds : bond 0.03251 ( 212) hydrogen bonds : angle 6.22810 ( 525) *********************** 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 88 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: J 4 ILE cc_start: 0.6573 (mp) cc_final: 0.6263 (mm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0595 time to fit residues: 8.6716 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.0070 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144572 restraints weight = 14424.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144006 restraints weight = 16142.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144006 restraints weight = 17282.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144006 restraints weight = 17284.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.144006 restraints weight = 17284.877| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3306 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= 0.145 Angle : 0.681 14.132 11889 Z= 0.336 Chirality : 0.048 0.182 1593 Planarity : 0.005 0.045 1503 Dihedral : 5.286 48.085 1260 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.03 % Favored : 87.55 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.03 (0.22), residues: 504 loop : -2.18 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.024 0.001 TYR K 34 PHE 0.009 0.001 PHE F 54 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8595) covalent geometry : angle 0.68137 (11889) hydrogen bonds : bond 0.03361 ( 212) hydrogen bonds : angle 6.07117 ( 525) *********************** 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 79 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.326 Fit side-chains REVERT: J 4 ILE cc_start: 0.6572 (mp) cc_final: 0.6327 (mm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0591 time to fit residues: 7.7809 Evaluate side-chains 71 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144479 restraints weight = 14571.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142990 restraints weight = 14998.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142877 restraints weight = 17083.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142874 restraints weight = 17457.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142874 restraints weight = 17461.820| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8595 Z= 0.147 Angle : 0.665 11.287 11889 Z= 0.329 Chirality : 0.049 0.161 1593 Planarity : 0.004 0.047 1503 Dihedral : 5.280 48.982 1260 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.11 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.02 (0.22), residues: 504 loop : -2.13 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.011 0.001 TYR L 73 PHE 0.020 0.001 PHE I 54 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8595) covalent geometry : angle 0.66494 (11889) hydrogen bonds : bond 0.03311 ( 212) hydrogen bonds : angle 6.00080 ( 525) *********************** 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 77 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.330 Fit side-chains REVERT: J 4 ILE cc_start: 0.6571 (mp) cc_final: 0.6338 (mm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0601 time to fit residues: 7.6789 Evaluate side-chains 68 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.161941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142177 restraints weight = 14318.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142177 restraints weight = 15653.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142177 restraints weight = 15653.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142177 restraints weight = 15653.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142177 restraints weight = 15653.397| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3637 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= 0.152 Angle : 0.680 11.345 11889 Z= 0.335 Chirality : 0.049 0.195 1593 Planarity : 0.004 0.047 1503 Dihedral : 5.278 50.189 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.11 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.03 (0.22), residues: 504 loop : -2.08 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.027 0.001 TYR K 34 PHE 0.013 0.001 PHE L 54 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8595) covalent geometry : angle 0.67964 (11889) hydrogen bonds : bond 0.03330 ( 212) hydrogen bonds : angle 5.99873 ( 525) *********************** 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 74 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.314 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0607 time to fit residues: 7.4453 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 : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.162487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.149038 restraints weight = 14209.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.147338 restraints weight = 22268.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.147669 restraints weight = 25504.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147371 restraints weight = 19858.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147511 restraints weight = 19224.230| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8595 Z= 0.146 Angle : 0.673 11.312 11889 Z= 0.334 Chirality : 0.048 0.155 1593 Planarity : 0.004 0.048 1503 Dihedral : 5.239 50.635 1260 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.03 % Favored : 87.55 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.05 (0.22), residues: 504 loop : -2.04 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.010 0.001 TYR L 73 PHE 0.013 0.001 PHE H 54 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8595) covalent geometry : angle 0.67315 (11889) hydrogen bonds : bond 0.03211 ( 212) hydrogen bonds : angle 5.88404 ( 525) *********************** 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 78 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.308 Fit side-chains REVERT: G 79 ASN cc_start: 0.8249 (t0) cc_final: 0.7682 (t0) REVERT: J 4 ILE cc_start: 0.6548 (mp) cc_final: 0.6235 (mm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0591 time to fit residues: 7.6059 Evaluate side-chains 62 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 32 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 27 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.164704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.152121 restraints weight = 14331.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150548 restraints weight = 20275.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150627 restraints weight = 22243.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150658 restraints weight = 17777.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150739 restraints weight = 16806.412| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8595 Z= 0.122 Angle : 0.663 12.713 11889 Z= 0.327 Chirality : 0.048 0.165 1593 Planarity : 0.004 0.047 1503 Dihedral : 5.042 51.266 1260 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.11 % Favored : 87.47 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.14 (0.22), residues: 504 loop : -1.97 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.025 0.001 TYR K 34 PHE 0.010 0.001 PHE F 54 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8595) covalent geometry : angle 0.66322 (11889) hydrogen bonds : bond 0.02902 ( 212) hydrogen bonds : angle 5.65610 ( 525) ********************** 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 : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0582 time to fit residues: 7.1591 Evaluate side-chains 60 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.0060 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN ** J 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.162645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.148423 restraints weight = 14106.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146893 restraints weight = 24072.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.147149 restraints weight = 25751.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147159 restraints weight = 20778.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.147288 restraints weight = 18586.533| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3953 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= 0.151 Angle : 0.685 11.200 11889 Z= 0.339 Chirality : 0.048 0.171 1593 Planarity : 0.004 0.048 1503 Dihedral : 5.152 50.861 1260 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.28 % Favored : 87.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.11 (0.22), residues: 504 loop : -2.00 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 32 TYR 0.010 0.001 TYR L 73 PHE 0.011 0.001 PHE H 54 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8595) covalent geometry : angle 0.68453 (11889) hydrogen bonds : bond 0.03202 ( 212) hydrogen bonds : angle 5.79322 ( 525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1176.50 seconds wall clock time: 21 minutes 13.25 seconds (1273.25 seconds total)