Starting phenix.real_space_refine on Mon Sep 23 21:42:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7saz_24959/09_2024/7saz_24959.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3743 2.51 5 N 896 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1740 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain: "B" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1723 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 456 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Time building chain proxies: 4.09, per 1000 atoms: 0.72 Number of scatterers: 5708 At special positions: 0 Unit cell: (68.224, 75.712, 114.816, 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 25 16.00 O 1044 8.00 N 896 7.00 C 3743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 674.8 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 77.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 28 through 67 removed outlier: 3.706A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.547A pdb=" N VAL A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 130 through 150 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.712A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 removed outlier: 3.853A pdb=" N MET B 11 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 3.673A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 132 through 152 removed outlier: 3.536A pdb=" N VAL B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.727A pdb=" N GLU B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 218 Processing helix chain 'C' and resid 8 through 33 removed outlier: 3.719A pdb=" N PHE C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 65 removed outlier: 3.551A pdb=" N ALA C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 33 Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.080A pdb=" N PHE D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 33 Processing helix chain 'E' and resid 43 through 65 removed outlier: 4.010A pdb=" N PHE E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 33 removed outlier: 4.684A pdb=" N TYR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 63 removed outlier: 3.959A pdb=" N PHE F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 33 Processing helix chain 'G' and resid 43 through 64 removed outlier: 4.079A pdb=" N PHE G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 175 434 hydrogen bonds defined for protein. 1281 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: 1.59 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1786 1.34 - 1.46: 897 1.46 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 5823 Sorted by residual: bond pdb=" CG LEU B 42 " pdb=" CD2 LEU B 42 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" CG1 ILE D 59 " pdb=" CD1 ILE D 59 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG MET B 11 " pdb=" SD MET B 11 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CA GLY F 40 " pdb=" C GLY F 40 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CG1 ILE F 59 " pdb=" CD1 ILE F 59 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 ... (remaining 5818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7673 1.98 - 3.96: 126 3.96 - 5.94: 14 5.94 - 7.92: 2 7.92 - 9.90: 1 Bond angle restraints: 7816 Sorted by residual: angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.89 -4.77 1.47e+00 4.63e-01 1.05e+01 angle pdb=" CA MET B 11 " pdb=" CB MET B 11 " pdb=" CG MET B 11 " ideal model delta sigma weight residual 114.10 107.86 6.24 2.00e+00 2.50e-01 9.74e+00 angle pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" C THR A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.20e+00 angle pdb=" C ILE A 12 " pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 ... (remaining 7811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 2962 15.25 - 30.50: 323 30.50 - 45.74: 90 45.74 - 60.99: 10 60.99 - 76.24: 6 Dihedral angle restraints: 3391 sinusoidal: 1355 harmonic: 2036 Sorted by residual: dihedral pdb=" CA MET A 113 " pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N GLY A 159 " pdb=" CA GLY A 159 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 665 0.050 - 0.101: 161 0.101 - 0.151: 12 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 840 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASP A 114 " pdb=" N ASP A 114 " pdb=" C ASP A 114 " pdb=" CB ASP A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PRO A 131 " pdb=" N PRO A 131 " pdb=" C PRO A 131 " pdb=" CB PRO A 131 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 837 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 130 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 131 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 130 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 131 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 66 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 67 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.017 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 348 2.73 - 3.27: 6021 3.27 - 3.82: 9696 3.82 - 4.36: 11341 4.36 - 4.90: 19652 Nonbonded interactions: 47058 Sorted by model distance: nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLU B 30 " model vdw 2.188 3.040 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE2 GLU C 56 " model vdw 2.237 3.120 nonbonded pdb=" ND2 ASN B 186 " pdb=" OE1 GLU B 190 " model vdw 2.285 3.120 nonbonded pdb=" O ILE F 59 " pdb=" OG SER F 63 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLU B 98 " pdb=" NZ LYS B 122 " model vdw 2.291 3.120 ... (remaining 47053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 220) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 10 through 65) selection = (chain 'D' and resid 10 through 65) selection = chain 'E' selection = (chain 'F' and resid 10 through 65) selection = (chain 'G' and resid 10 through 65) } 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: 0.890 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.004 0.064 5823 Z= 0.271 Angle : 0.628 9.899 7816 Z= 0.354 Chirality : 0.041 0.252 840 Planarity : 0.004 0.077 997 Dihedral : 13.698 76.236 2097 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.31), residues: 708 helix: 1.14 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -3.14 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 34 HIS 0.010 0.002 HIS G 33 PHE 0.013 0.001 PHE A 123 TYR 0.020 0.002 TYR B 216 ARG 0.015 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.579 Fit side-chains REVERT: A 173 ASP cc_start: 0.8789 (m-30) cc_final: 0.8425 (m-30) REVERT: B 100 MET cc_start: 0.8448 (mmp) cc_final: 0.8242 (mmt) REVERT: B 203 MET cc_start: 0.7223 (tpp) cc_final: 0.6960 (tpt) REVERT: B 207 ASP cc_start: 0.7846 (m-30) cc_final: 0.7641 (m-30) REVERT: C 10 LYS cc_start: 0.8166 (pptt) cc_final: 0.7060 (mptt) REVERT: D 14 MET cc_start: 0.8412 (ttm) cc_final: 0.8189 (ttp) REVERT: F 14 MET cc_start: 0.7609 (ttm) cc_final: 0.7184 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.1909 time to fit residues: 166.4739 Evaluate side-chains 94 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 121 GLN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5823 Z= 0.172 Angle : 0.501 6.282 7816 Z= 0.277 Chirality : 0.038 0.178 840 Planarity : 0.003 0.047 997 Dihedral : 4.440 26.114 752 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.55 % Allowed : 12.05 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.31), residues: 708 helix: 1.88 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.08 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 34 HIS 0.004 0.001 HIS D 33 PHE 0.011 0.001 PHE C 47 TYR 0.015 0.001 TYR E 16 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7329 (p0) cc_final: 0.6774 (m-40) REVERT: B 73 GLU cc_start: 0.7826 (pp20) cc_final: 0.7584 (tm-30) REVERT: B 100 MET cc_start: 0.8291 (mmp) cc_final: 0.8021 (mmt) REVERT: D 14 MET cc_start: 0.8336 (ttm) cc_final: 0.8078 (ttp) outliers start: 15 outliers final: 3 residues processed: 103 average time/residue: 1.2575 time to fit residues: 135.0948 Evaluate side-chains 84 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 102 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5823 Z= 0.171 Angle : 0.476 5.953 7816 Z= 0.263 Chirality : 0.038 0.191 840 Planarity : 0.003 0.046 997 Dihedral : 4.205 25.030 752 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.87 % Allowed : 15.96 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 708 helix: 2.16 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.08 (0.40), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7250 (p0) cc_final: 0.6744 (m-40) REVERT: A 61 GLU cc_start: 0.7362 (tp30) cc_final: 0.6934 (tm-30) REVERT: A 219 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7121 (mtp) REVERT: B 73 GLU cc_start: 0.7828 (pp20) cc_final: 0.7611 (tm-30) REVERT: D 14 MET cc_start: 0.8294 (ttm) cc_final: 0.8021 (ttp) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 1.1339 time to fit residues: 118.6901 Evaluate side-chains 88 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 102 GLN B 172 ASN B 213 GLN D 13 GLN G 33 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5823 Z= 0.346 Angle : 0.561 6.807 7816 Z= 0.301 Chirality : 0.042 0.311 840 Planarity : 0.003 0.046 997 Dihedral : 4.398 22.402 752 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.57 % Allowed : 16.81 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.31), residues: 708 helix: 1.94 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.004 0.001 HIS G 33 PHE 0.013 0.001 PHE D 60 TYR 0.020 0.002 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 219 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7248 (mtp) REVERT: B 73 GLU cc_start: 0.7847 (pp20) cc_final: 0.7599 (tm-30) REVERT: B 79 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8153 (mtpp) REVERT: D 14 MET cc_start: 0.8311 (ttm) cc_final: 0.8089 (ttp) outliers start: 21 outliers final: 9 residues processed: 101 average time/residue: 1.2617 time to fit residues: 132.9144 Evaluate side-chains 98 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.1980 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 170 ASN B 172 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5823 Z= 0.144 Angle : 0.454 6.446 7816 Z= 0.252 Chirality : 0.037 0.230 840 Planarity : 0.003 0.049 997 Dihedral : 4.100 25.086 752 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.38 % Allowed : 19.35 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 708 helix: 2.29 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 34 HIS 0.003 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7247 (p0) cc_final: 0.6684 (m-40) REVERT: A 111 GLN cc_start: 0.7854 (tt0) cc_final: 0.7622 (pt0) REVERT: A 173 ASP cc_start: 0.8780 (m-30) cc_final: 0.8522 (m-30) REVERT: A 219 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7403 (mtp) REVERT: B 79 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8123 (mtpp) REVERT: D 14 MET cc_start: 0.8284 (ttm) cc_final: 0.8024 (ttp) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 1.2177 time to fit residues: 133.5919 Evaluate side-chains 98 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5823 Z= 0.154 Angle : 0.491 14.199 7816 Z= 0.262 Chirality : 0.039 0.370 840 Planarity : 0.003 0.049 997 Dihedral : 3.993 23.850 752 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.04 % Allowed : 20.71 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.31), residues: 708 helix: 2.37 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 PHE 0.008 0.001 PHE D 60 TYR 0.014 0.001 TYR E 16 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8750 (m-30) cc_final: 0.8468 (m-30) REVERT: B 73 GLU cc_start: 0.7779 (pp20) cc_final: 0.7459 (tm-30) REVERT: B 79 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8115 (mtpp) REVERT: C 48 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8545 (mt) REVERT: D 14 MET cc_start: 0.8255 (ttm) cc_final: 0.7997 (ttp) outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 1.1543 time to fit residues: 129.3619 Evaluate side-chains 100 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5823 Z= 0.240 Angle : 0.526 13.012 7816 Z= 0.279 Chirality : 0.041 0.437 840 Planarity : 0.003 0.050 997 Dihedral : 4.074 23.268 752 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.87 % Allowed : 22.58 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.31), residues: 708 helix: 2.25 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.88 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.018 0.001 TYR E 16 ARG 0.006 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8866 (m-30) cc_final: 0.8612 (m-30) REVERT: B 73 GLU cc_start: 0.7805 (pp20) cc_final: 0.7516 (tm-30) REVERT: B 79 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8092 (mtpp) REVERT: C 48 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8536 (mt) REVERT: D 14 MET cc_start: 0.8276 (ttm) cc_final: 0.7988 (ttp) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 1.2252 time to fit residues: 131.8095 Evaluate side-chains 99 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5823 Z= 0.185 Angle : 0.500 11.396 7816 Z= 0.270 Chirality : 0.040 0.392 840 Planarity : 0.003 0.052 997 Dihedral : 4.004 23.936 752 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.87 % Allowed : 23.09 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.31), residues: 708 helix: 2.30 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.85 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.004 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8827 (m-30) cc_final: 0.8568 (m-30) REVERT: B 73 GLU cc_start: 0.7800 (pp20) cc_final: 0.7515 (tm-30) REVERT: B 79 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8091 (mtpp) REVERT: C 48 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8538 (mt) REVERT: D 14 MET cc_start: 0.8275 (ttm) cc_final: 0.7991 (ttp) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 1.2264 time to fit residues: 129.4515 Evaluate side-chains 98 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5823 Z= 0.184 Angle : 0.501 11.916 7816 Z= 0.270 Chirality : 0.040 0.424 840 Planarity : 0.003 0.052 997 Dihedral : 3.982 23.728 752 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 22.92 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.31), residues: 708 helix: 2.29 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.82 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.005 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8810 (m-30) cc_final: 0.8537 (m-30) REVERT: B 73 GLU cc_start: 0.7793 (pp20) cc_final: 0.7519 (tm-30) REVERT: B 79 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8076 (mtpp) REVERT: B 102 GLN cc_start: 0.8440 (pp30) cc_final: 0.7794 (pp30) REVERT: C 48 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8523 (mt) REVERT: D 14 MET cc_start: 0.8251 (ttm) cc_final: 0.7925 (ttp) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 1.1388 time to fit residues: 121.6258 Evaluate side-chains 100 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5823 Z= 0.217 Angle : 0.522 11.684 7816 Z= 0.281 Chirality : 0.041 0.440 840 Planarity : 0.003 0.052 997 Dihedral : 3.986 23.270 752 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 23.60 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 708 helix: 2.25 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.83 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 PHE 0.010 0.001 PHE D 60 TYR 0.016 0.001 TYR E 16 ARG 0.007 0.001 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8841 (m-30) cc_final: 0.8588 (m-30) REVERT: B 73 GLU cc_start: 0.7784 (pp20) cc_final: 0.7440 (tm-30) REVERT: B 79 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8066 (mtpp) REVERT: B 102 GLN cc_start: 0.8454 (pp30) cc_final: 0.7872 (pp30) REVERT: C 48 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8538 (mt) REVERT: D 14 MET cc_start: 0.8254 (ttm) cc_final: 0.7927 (ttp) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 1.1688 time to fit residues: 124.6849 Evaluate side-chains 97 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112491 restraints weight = 6781.347| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.27 r_work: 0.3107 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5823 Z= 0.163 Angle : 0.509 15.776 7816 Z= 0.270 Chirality : 0.041 0.505 840 Planarity : 0.003 0.053 997 Dihedral : 3.907 23.787 752 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 22.92 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.31), residues: 708 helix: 2.35 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.78 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 34 HIS 0.004 0.001 HIS G 33 PHE 0.009 0.001 PHE D 60 TYR 0.015 0.001 TYR E 16 ARG 0.007 0.001 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.59 seconds wall clock time: 45 minutes 5.23 seconds (2705.23 seconds total)