Starting phenix.real_space_refine on Mon May 6 14:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/05_2024/8xbw_38231.pdb" } resolution = 2.89 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= 0.000 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 6 5.16 5 C 1573 2.51 5 N 501 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 2671 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 2.17, per 1000 atoms: 0.81 Number of scatterers: 2671 At special positions: 0 Unit cell: (82.68, 71.02, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 36 15.00 O 555 8.00 N 501 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 372.9 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 454 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 73.6% alpha, 1.7% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.807A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.866A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 123 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 678 1.33 - 1.45: 614 1.45 - 1.57: 1412 1.57 - 1.69: 71 1.69 - 1.81: 9 Bond restraints: 2784 Sorted by residual: bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta sigma weight residual 1.536 1.578 -0.042 1.42e-02 4.96e+03 8.73e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG F 19 " pdb=" NH2 ARG F 19 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CZ ARG F 23 " pdb=" NH2 ARG F 23 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.28e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.69: 207 105.69 - 113.03: 1512 113.03 - 120.36: 1163 120.36 - 127.69: 954 127.69 - 135.03: 60 Bond angle restraints: 3896 Sorted by residual: angle pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 112.60 106.96 5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.97 121.08 -7.11 1.28e+00 6.10e-01 3.09e+01 angle pdb=" CA ASN F 25 " pdb=" C ASN F 25 " pdb=" N ILE F 26 " ideal model delta sigma weight residual 118.47 125.19 -6.72 1.26e+00 6.30e-01 2.85e+01 angle pdb=" C HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta sigma weight residual 109.51 117.73 -8.22 1.71e+00 3.42e-01 2.31e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.70 4.40 9.70e-01 1.06e+00 2.05e+01 ... (remaining 3891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1208 16.98 - 33.96: 184 33.96 - 50.94: 153 50.94 - 67.92: 64 67.92 - 84.90: 3 Dihedral angle restraints: 1612 sinusoidal: 911 harmonic: 701 Sorted by residual: dihedral pdb=" CA GLY L 32 " pdb=" C GLY L 32 " pdb=" N ILE L 33 " pdb=" CA ILE L 33 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N LYS F 20 " pdb=" CA LYS F 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C HIS E 39 " pdb=" N HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta harmonic sigma weight residual -122.60 -131.94 9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 1609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 424 0.102 - 0.204: 18 0.204 - 0.305: 1 0.305 - 0.407: 0 0.407 - 0.509: 1 Chirality restraints: 444 Sorted by residual: chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P DA I 51 " pdb=" OP1 DA I 51 " pdb=" OP2 DA I 51 " pdb=" O5' DA I 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.64 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 441 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 51 " -0.076 2.00e-02 2.50e+03 3.09e-02 2.62e+01 pdb=" N9 DA I 51 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 51 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 51 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 51 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DA I 51 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA I 51 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 51 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA I 51 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA I 51 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DA I 51 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 39 " -0.043 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS E 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS E 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 39 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 23 " 0.060 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO L 24 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 24 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 24 " 0.048 5.00e-02 4.00e+02 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 1 1.90 - 2.65: 54 2.65 - 3.40: 3563 3.40 - 4.15: 7271 4.15 - 4.90: 11510 Nonbonded interactions: 22399 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 90 " model vdw 1.155 2.520 nonbonded pdb=" NH2 ARG E 40 " pdb=" C2 DT J 90 " model vdw 2.155 3.340 nonbonded pdb=" O GLN L 23 " pdb=" N VAL L 49 " model vdw 2.220 2.520 nonbonded pdb=" OD1 ASP E 77 " pdb=" NZ LYS L 73 " model vdw 2.273 2.520 nonbonded pdb=" NZ LYS L 57 " pdb=" OD1 ASP L 72 " model vdw 2.299 2.520 ... (remaining 22394 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: 1.090 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: 5.330 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.810 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.006 0.073 2784 Z= 0.376 Angle : 1.060 8.216 3896 Z= 0.729 Chirality : 0.054 0.509 444 Planarity : 0.009 0.089 371 Dihedral : 23.744 84.903 1158 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -0.65 (0.47), residues: 236 helix: -0.12 (0.36), residues: 159 sheet: None (None), residues: 0 loop : -0.82 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.004 HIS E 39 PHE 0.009 0.001 PHE F 61 TYR 0.016 0.002 TYR F 51 ARG 0.006 0.001 ARG L 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9230 (m-30) cc_final: 0.8979 (p0) REVERT: F 43 VAL cc_start: 0.7864 (t) cc_final: 0.7433 (t) REVERT: L 73 LYS cc_start: 0.6764 (mttt) cc_final: 0.6412 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.2031 time to fit residues: 141.2241 Evaluate side-chains 74 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2784 Z= 0.295 Angle : 0.843 13.163 3896 Z= 0.457 Chirality : 0.044 0.168 444 Planarity : 0.006 0.044 371 Dihedral : 26.301 61.980 663 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 10.40 % Allowed : 27.23 % Favored : 62.38 % 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: 0.12 (0.52), residues: 236 helix: 0.49 (0.39), residues: 166 sheet: None (None), residues: 0 loop : -0.70 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS E 39 PHE 0.014 0.003 PHE F 61 TYR 0.028 0.003 TYR E 99 ARG 0.005 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9294 (m-30) cc_final: 0.9073 (m-30) REVERT: E 104 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8895 (t80) REVERT: E 105 GLU cc_start: 0.9140 (tp30) cc_final: 0.8850 (mm-30) REVERT: F 90 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8286 (mm) REVERT: L 46 PHE cc_start: 0.6008 (m-80) cc_final: 0.5689 (m-80) outliers start: 21 outliers final: 9 residues processed: 93 average time/residue: 1.0235 time to fit residues: 97.5649 Evaluate side-chains 78 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain L residue 34 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.7332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2784 Z= 0.293 Angle : 0.886 12.243 3896 Z= 0.463 Chirality : 0.044 0.170 444 Planarity : 0.006 0.051 371 Dihedral : 25.838 69.378 663 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 30.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 8.42 % Allowed : 33.17 % Favored : 58.42 % 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: -0.41 (0.50), residues: 236 helix: 0.33 (0.38), residues: 166 sheet: None (None), residues: 0 loop : -1.57 (0.63), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 47 PHE 0.010 0.002 PHE E 104 TYR 0.012 0.002 TYR E 54 ARG 0.005 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8794 (t80) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.6999 time to fit residues: 62.4852 Evaluate side-chains 79 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain L residue 34 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.8528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2784 Z= 0.312 Angle : 0.937 12.304 3896 Z= 0.473 Chirality : 0.044 0.185 444 Planarity : 0.005 0.037 371 Dihedral : 25.510 74.163 663 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 7.92 % Allowed : 36.14 % Favored : 55.94 % 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: -0.97 (0.49), residues: 236 helix: -0.08 (0.37), residues: 166 sheet: None (None), residues: 0 loop : -1.81 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 113 PHE 0.012 0.002 PHE F 61 TYR 0.020 0.003 TYR E 99 ARG 0.003 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 TYR cc_start: 0.8894 (t80) cc_final: 0.8640 (t80) REVERT: E 104 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8893 (t80) REVERT: F 72 TYR cc_start: 0.8639 (m-80) cc_final: 0.8404 (m-10) REVERT: F 92 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7809 (ttt180) REVERT: L 43 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8477 (pp20) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.8428 time to fit residues: 74.7636 Evaluate side-chains 82 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2784 Z= 0.289 Angle : 0.952 13.152 3896 Z= 0.483 Chirality : 0.047 0.197 444 Planarity : 0.006 0.052 371 Dihedral : 25.460 76.690 663 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 7.43 % Allowed : 41.58 % Favored : 50.99 % 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: -1.13 (0.49), residues: 236 helix: -0.23 (0.38), residues: 159 sheet: None (None), residues: 0 loop : -1.67 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.013 0.002 PHE E 67 TYR 0.018 0.002 TYR E 54 ARG 0.005 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8889 (t80) REVERT: F 72 TYR cc_start: 0.8639 (m-80) cc_final: 0.8418 (m-80) REVERT: L 34 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7858 (t0) outliers start: 15 outliers final: 7 residues processed: 85 average time/residue: 0.7316 time to fit residues: 64.4942 Evaluate side-chains 78 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain L residue 34 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 11 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: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.9569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2784 Z= 0.281 Angle : 1.076 17.353 3896 Z= 0.519 Chirality : 0.051 0.263 444 Planarity : 0.005 0.038 371 Dihedral : 25.361 77.229 663 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 7.43 % Allowed : 42.57 % Favored : 50.00 % 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: -1.12 (0.48), residues: 236 helix: -0.35 (0.37), residues: 158 sheet: None (None), residues: 0 loop : -1.35 (0.61), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 39 PHE 0.026 0.003 PHE F 61 TYR 0.048 0.004 TYR E 99 ARG 0.004 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9019 (mtp85) cc_final: 0.8604 (ptp-110) REVERT: E 100 LEU cc_start: 0.9474 (pp) cc_final: 0.9175 (pt) REVERT: E 104 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8793 (t80) REVERT: E 122 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.6144 (pttt) REVERT: F 52 GLU cc_start: 0.8772 (pm20) cc_final: 0.8533 (pm20) REVERT: F 60 VAL cc_start: 0.9096 (m) cc_final: 0.8729 (p) REVERT: F 72 TYR cc_start: 0.8532 (m-80) cc_final: 0.8330 (m-80) REVERT: F 92 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7781 (tmt170) REVERT: L 70 LYS cc_start: 0.7217 (ptpp) cc_final: 0.6827 (tptp) outliers start: 15 outliers final: 4 residues processed: 85 average time/residue: 0.8081 time to fit residues: 70.8610 Evaluate side-chains 76 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 1.0115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2784 Z= 0.284 Angle : 1.072 15.992 3896 Z= 0.532 Chirality : 0.049 0.223 444 Planarity : 0.005 0.039 371 Dihedral : 25.323 77.484 663 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.46 % Allowed : 48.51 % Favored : 47.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.48), residues: 236 helix: -0.76 (0.37), residues: 161 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 47 PHE 0.013 0.002 PHE E 67 TYR 0.023 0.003 TYR E 99 ARG 0.004 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9035 (mtp85) cc_final: 0.8538 (ptp-110) REVERT: E 104 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8746 (t80) REVERT: F 92 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7927 (tmt170) REVERT: L 70 LYS cc_start: 0.7309 (ptpp) cc_final: 0.6931 (tptp) outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 0.7936 time to fit residues: 65.5219 Evaluate side-chains 75 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 1.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2784 Z= 0.306 Angle : 1.147 16.878 3896 Z= 0.560 Chirality : 0.052 0.231 444 Planarity : 0.006 0.046 371 Dihedral : 25.337 78.775 663 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 29.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.93 % Allowed : 48.51 % Favored : 44.55 % 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: -1.98 (0.48), residues: 236 helix: -0.98 (0.37), residues: 166 sheet: None (None), residues: 0 loop : -1.77 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 47 PHE 0.022 0.003 PHE F 61 TYR 0.033 0.003 TYR E 99 ARG 0.003 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: E 49 ARG cc_start: 0.8983 (mtp85) cc_final: 0.8378 (ptp-110) REVERT: E 52 ARG cc_start: 0.8551 (ptp-110) cc_final: 0.8264 (ptt-90) REVERT: E 104 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8693 (t80) REVERT: F 23 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8443 (pmm-80) REVERT: F 44 LYS cc_start: 0.8324 (tmmt) cc_final: 0.8052 (pptt) REVERT: F 72 TYR cc_start: 0.8585 (m-80) cc_final: 0.8349 (m-10) REVERT: F 92 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8066 (ttt180) REVERT: L 70 LYS cc_start: 0.7454 (ptpp) cc_final: 0.6993 (tptp) outliers start: 14 outliers final: 5 residues processed: 86 average time/residue: 0.8204 time to fit residues: 72.7347 Evaluate side-chains 78 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 1.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2784 Z= 0.318 Angle : 1.179 17.668 3896 Z= 0.578 Chirality : 0.054 0.229 444 Planarity : 0.006 0.051 371 Dihedral : 25.369 80.179 663 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.45 % Allowed : 49.01 % Favored : 45.54 % 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: -1.72 (0.50), residues: 236 helix: -0.75 (0.38), residues: 167 sheet: None (None), residues: 0 loop : -1.80 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 39 PHE 0.027 0.003 PHE F 61 TYR 0.042 0.003 TYR E 99 ARG 0.004 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: E 41 TYR cc_start: 0.6105 (m-10) cc_final: 0.5594 (m-10) REVERT: E 90 MET cc_start: 0.7912 (ttp) cc_final: 0.7500 (tpp) REVERT: E 110 CYS cc_start: 0.8303 (t) cc_final: 0.7996 (p) REVERT: E 123 ASP cc_start: 0.7270 (m-30) cc_final: 0.6826 (t0) REVERT: F 23 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8455 (pmm-80) REVERT: F 92 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8075 (ttt180) REVERT: L 60 LEU cc_start: 0.9066 (pp) cc_final: 0.8785 (pt) REVERT: L 70 LYS cc_start: 0.7421 (ptpp) cc_final: 0.7007 (tptp) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.8658 time to fit residues: 72.2766 Evaluate side-chains 75 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 1.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 2784 Z= 0.326 Angle : 1.234 17.015 3896 Z= 0.608 Chirality : 0.058 0.352 444 Planarity : 0.007 0.054 371 Dihedral : 25.396 80.662 663 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 31.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.48 % Allowed : 51.49 % Favored : 46.04 % 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: -2.13 (0.49), residues: 236 helix: -1.08 (0.37), residues: 167 sheet: None (None), residues: 0 loop : -1.89 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.028 0.004 PHE F 61 TYR 0.050 0.004 TYR E 99 ARG 0.008 0.001 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 ASP cc_start: 0.7228 (m-30) cc_final: 0.6883 (m-30) REVERT: F 92 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: L 60 LEU cc_start: 0.9014 (pp) cc_final: 0.8787 (pt) REVERT: L 70 LYS cc_start: 0.7491 (ptpp) cc_final: 0.7140 (tptp) REVERT: L 75 LEU cc_start: 0.8467 (mm) cc_final: 0.8068 (pp) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.7538 time to fit residues: 55.4265 Evaluate side-chains 68 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.072584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051919 restraints weight = 12296.321| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.61 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 1.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 2784 Z= 0.345 Angle : 1.276 18.522 3896 Z= 0.630 Chirality : 0.058 0.332 444 Planarity : 0.007 0.053 371 Dihedral : 25.386 80.911 663 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 30.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.48 % Allowed : 51.98 % Favored : 45.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.48), residues: 236 helix: -1.32 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -2.00 (0.64), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.034 0.003 PHE F 61 TYR 0.053 0.003 TYR E 99 ARG 0.005 0.001 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.43 seconds wall clock time: 31 minutes 12.71 seconds (1872.71 seconds total)