Starting phenix.real_space_refine on Fri Dec 8 01:08:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stf_25427/12_2023/7stf_25427.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 23 5.16 5 C 4030 2.51 5 N 1104 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ASP 153": "OD1" <-> "OD2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 189": "OE1" <-> "OE2" Residue "L PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 6": "NH1" <-> "NH2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6414 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 62 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1663 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Time building chain proxies: 3.97, per 1000 atoms: 0.62 Number of scatterers: 6414 At special positions: 0 Unit cell: (70.052, 64.144, 145.168, 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 23 16.00 O 1257 8.00 N 1104 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 12.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.652A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.861A pdb=" N TYR L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.616A pdb=" N GLN A 54 " --> pdb=" O TRP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.633A pdb=" N THR A 228 " --> pdb=" O THR A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.654A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.749A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.865A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.786A pdb=" N THR L 74 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.910A pdb=" N PHE L 118 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU L 137 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE L 120 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.755A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 168 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.959A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB4, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB5, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.624A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.777A pdb=" N PHE B 90 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.713A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 417 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: 1.58 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2076 1.34 - 1.47: 1710 1.47 - 1.59: 2755 1.59 - 1.72: 0 1.72 - 1.85: 32 Bond restraints: 6573 Sorted by residual: bond pdb=" C ARG H 98 " pdb=" N ALA H 99 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.97e-02 2.58e+03 9.41e+00 bond pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " ideal model delta sigma weight residual 1.534 1.488 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.27e-02 6.20e+03 5.53e+00 ... (remaining 6568 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.52: 160 105.52 - 112.69: 3344 112.69 - 119.85: 2246 119.85 - 127.02: 3074 127.02 - 134.18: 111 Bond angle restraints: 8935 Sorted by residual: angle pdb=" C PHE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.80 106.36 15.44 2.44e+00 1.68e-01 4.00e+01 angle pdb=" C SER L 52 " pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 121.72 131.19 -9.47 1.54e+00 4.22e-01 3.78e+01 angle pdb=" C GLN L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta sigma weight residual 121.54 132.85 -11.31 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.42 113.90 8.52 1.55e+00 4.16e-01 3.02e+01 angle pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" C TYR L 92 " ideal model delta sigma weight residual 110.80 122.19 -11.39 2.13e+00 2.20e-01 2.86e+01 ... (remaining 8930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3403 16.18 - 32.36: 405 32.36 - 48.53: 79 48.53 - 64.71: 15 64.71 - 80.89: 15 Dihedral angle restraints: 3917 sinusoidal: 1545 harmonic: 2372 Sorted by residual: dihedral pdb=" CA SER L 91 " pdb=" C SER L 91 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " ideal model delta harmonic sigma weight residual -180.00 -124.10 -55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASP A 29 " pdb=" C ASP A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA ASN H 77 " pdb=" C ASN H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta harmonic sigma weight residual -180.00 -140.14 -39.86 0 5.00e+00 4.00e-02 6.36e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 882 0.105 - 0.209: 82 0.209 - 0.314: 1 0.314 - 0.418: 1 0.418 - 0.523: 1 Chirality restraints: 967 Sorted by residual: chirality pdb=" CG LEU L 46 " pdb=" CB LEU L 46 " pdb=" CD1 LEU L 46 " pdb=" CD2 LEU L 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA MET H 52 " pdb=" N MET H 52 " pdb=" C MET H 52 " pdb=" CB MET H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 964 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 125 " -0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO H 126 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU A 160 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 161 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 109 " 0.031 2.00e-02 2.50e+03 2.12e-02 8.98e+00 pdb=" CG TYR H 109 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR H 109 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 109 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 109 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 134 2.58 - 3.16: 6039 3.16 - 3.74: 10420 3.74 - 4.32: 14730 4.32 - 4.90: 23459 Nonbonded interactions: 54782 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O ASP L 70 " model vdw 1.998 2.520 nonbonded pdb=" OG SER B 31 " pdb=" O HIS B 33 " model vdw 2.054 2.440 nonbonded pdb=" O HIS H 208 " pdb=" OG SER H 211 " model vdw 2.115 2.440 nonbonded pdb=" OG SER H 75 " pdb=" OD1 ASN H 77 " model vdw 2.120 2.440 nonbonded pdb=" O VAL H 2 " pdb=" ND2 ASN H 101 " model vdw 2.164 2.520 ... (remaining 54777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.710 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.830 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.009 0.085 6573 Z= 0.599 Angle : 1.206 15.438 8935 Z= 0.665 Chirality : 0.062 0.523 967 Planarity : 0.007 0.093 1161 Dihedral : 15.262 80.889 2376 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 20.12 % Favored : 79.13 % Rotamer: Outliers : 0.14 % Allowed : 0.85 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.27), residues: 805 helix: -1.22 (0.53), residues: 87 sheet: -1.69 (0.34), residues: 211 loop : -3.30 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 162 HIS 0.012 0.003 HIS H 57 PHE 0.044 0.004 PHE L 95 TYR 0.050 0.005 TYR H 109 ARG 0.013 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.741 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2565 time to fit residues: 31.5324 Evaluate side-chains 72 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.286 Angle : 0.902 10.549 8935 Z= 0.479 Chirality : 0.050 0.202 967 Planarity : 0.006 0.059 1161 Dihedral : 8.538 71.390 896 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.77 % Favored : 82.86 % Rotamer: Outliers : 0.71 % Allowed : 10.38 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.28), residues: 805 helix: -0.70 (0.54), residues: 95 sheet: -1.59 (0.34), residues: 218 loop : -3.33 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 204 HIS 0.010 0.002 HIS B 51 PHE 0.032 0.003 PHE L 95 TYR 0.026 0.003 TYR L 49 ARG 0.005 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.734 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 92 average time/residue: 0.2084 time to fit residues: 25.0925 Evaluate side-chains 77 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0598 time to fit residues: 1.5580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 60 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 163 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6573 Z= 0.238 Angle : 0.826 10.666 8935 Z= 0.436 Chirality : 0.048 0.263 967 Planarity : 0.006 0.061 1161 Dihedral : 8.013 71.245 896 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.53 % Favored : 84.22 % Rotamer: Outliers : 1.42 % Allowed : 14.51 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.28), residues: 805 helix: -0.52 (0.55), residues: 96 sheet: -1.43 (0.37), residues: 192 loop : -3.24 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 PHE 0.016 0.002 PHE H 129 TYR 0.033 0.002 TYR L 175 ARG 0.018 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.774 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.1954 time to fit residues: 23.7923 Evaluate side-chains 71 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0652 time to fit residues: 1.4321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6573 Z= 0.380 Angle : 0.883 11.487 8935 Z= 0.470 Chirality : 0.050 0.264 967 Planarity : 0.006 0.057 1161 Dihedral : 8.212 70.071 896 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 17.52 % Favored : 82.11 % Rotamer: Outliers : 2.56 % Allowed : 16.50 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.28), residues: 805 helix: -0.72 (0.52), residues: 102 sheet: -1.55 (0.34), residues: 223 loop : -3.39 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 110 HIS 0.009 0.002 HIS B 51 PHE 0.034 0.003 PHE L 141 TYR 0.030 0.003 TYR L 49 ARG 0.023 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 87 average time/residue: 0.2121 time to fit residues: 24.1262 Evaluate side-chains 82 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0973 time to fit residues: 2.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6573 Z= 0.293 Angle : 0.833 10.429 8935 Z= 0.440 Chirality : 0.049 0.278 967 Planarity : 0.006 0.057 1161 Dihedral : 7.957 69.262 896 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.15 % Favored : 83.48 % Rotamer: Outliers : 1.56 % Allowed : 18.78 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.28), residues: 805 helix: -0.62 (0.53), residues: 102 sheet: -1.59 (0.32), residues: 239 loop : -3.48 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 PHE 0.020 0.002 PHE L 141 TYR 0.024 0.002 TYR A 84 ARG 0.015 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.762 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.2197 time to fit residues: 24.3276 Evaluate side-chains 76 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0695 time to fit residues: 1.4805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0030 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 0.0980 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6573 Z= 0.277 Angle : 0.825 10.272 8935 Z= 0.433 Chirality : 0.048 0.248 967 Planarity : 0.006 0.055 1161 Dihedral : 7.771 69.071 896 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.65 % Favored : 83.11 % Rotamer: Outliers : 1.28 % Allowed : 20.48 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.28), residues: 805 helix: -0.51 (0.53), residues: 103 sheet: -1.31 (0.34), residues: 219 loop : -3.48 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 PHE 0.015 0.002 PHE L 141 TYR 0.021 0.002 TYR A 84 ARG 0.012 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.743 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.1937 time to fit residues: 20.8335 Evaluate side-chains 71 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0765 time to fit residues: 1.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6573 Z= 0.214 Angle : 0.779 9.873 8935 Z= 0.405 Chirality : 0.046 0.187 967 Planarity : 0.006 0.076 1161 Dihedral : 7.394 69.620 896 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.54 % Favored : 86.21 % Rotamer: Outliers : 0.85 % Allowed : 21.62 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.28), residues: 805 helix: -0.14 (0.55), residues: 102 sheet: -1.38 (0.32), residues: 237 loop : -3.42 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 PHE 0.013 0.002 PHE H 129 TYR 0.021 0.002 TYR A 84 ARG 0.010 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.1945 time to fit residues: 21.4567 Evaluate side-chains 75 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0605 time to fit residues: 1.2128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 6573 Z= 0.385 Angle : 0.872 11.333 8935 Z= 0.460 Chirality : 0.050 0.224 967 Planarity : 0.007 0.073 1161 Dihedral : 7.824 68.172 896 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.37 % Allowed : 17.89 % Favored : 81.74 % Rotamer: Outliers : 1.28 % Allowed : 21.48 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.28), residues: 805 helix: -0.41 (0.53), residues: 103 sheet: -1.14 (0.34), residues: 217 loop : -3.47 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 110 HIS 0.008 0.002 HIS B 51 PHE 0.015 0.002 PHE B 76 TYR 0.033 0.003 TYR H 95 ARG 0.014 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.1965 time to fit residues: 21.4225 Evaluate side-chains 81 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0709 time to fit residues: 1.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6573 Z= 0.263 Angle : 0.823 10.004 8935 Z= 0.430 Chirality : 0.048 0.190 967 Planarity : 0.007 0.093 1161 Dihedral : 7.556 67.721 896 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.90 % Favored : 83.85 % Rotamer: Outliers : 0.57 % Allowed : 22.19 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.28), residues: 805 helix: -0.12 (0.55), residues: 101 sheet: -1.39 (0.32), residues: 249 loop : -3.42 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 110 HIS 0.008 0.001 HIS B 51 PHE 0.014 0.002 PHE H 129 TYR 0.022 0.002 TYR H 95 ARG 0.006 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.2277 time to fit residues: 24.0641 Evaluate side-chains 75 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0710 time to fit residues: 1.3666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6573 Z= 0.254 Angle : 0.818 9.956 8935 Z= 0.425 Chirality : 0.047 0.182 967 Planarity : 0.006 0.072 1161 Dihedral : 7.412 66.517 896 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 17.39 % Favored : 82.36 % Rotamer: Outliers : 0.57 % Allowed : 22.33 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.28), residues: 805 helix: -0.22 (0.54), residues: 101 sheet: -1.43 (0.31), residues: 245 loop : -3.36 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 110 HIS 0.009 0.001 HIS B 51 PHE 0.013 0.002 PHE B 76 TYR 0.029 0.002 TYR H 95 ARG 0.019 0.001 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 80 average time/residue: 0.1970 time to fit residues: 21.0814 Evaluate side-chains 76 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0651 time to fit residues: 1.1770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 55 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 ASN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** 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 = 0.4578 r_free = 0.4578 target = 0.144740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.110542 restraints weight = 13203.564| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.17 r_work: 0.3929 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6573 Z= 0.217 Angle : 0.786 9.661 8935 Z= 0.406 Chirality : 0.047 0.173 967 Planarity : 0.006 0.072 1161 Dihedral : 7.281 64.954 896 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.41 % Favored : 85.34 % Rotamer: Outliers : 0.28 % Allowed : 22.76 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.28), residues: 805 helix: -0.24 (0.53), residues: 101 sheet: -1.44 (0.31), residues: 258 loop : -3.28 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 110 HIS 0.008 0.001 HIS B 51 PHE 0.012 0.001 PHE H 129 TYR 0.026 0.002 TYR H 95 ARG 0.013 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.08 seconds wall clock time: 35 minutes 6.36 seconds (2106.36 seconds total)