Starting phenix.real_space_refine on Sun Mar 10 14:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.715 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/03_2024/8g2v_29682.pdb" } resolution = 2.715 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= 0.003 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 10 5.16 5 C 1030 2.51 5 N 320 2.21 5 O 300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1660 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "B" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "C" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "F" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "G" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "H" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "I" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "J" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Time building chain proxies: 1.20, per 1000 atoms: 0.72 Number of scatterers: 1660 At special positions: 0 Unit cell: (61.523, 55.131, 39.151, 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 10 16.00 O 300 8.00 N 320 7.00 C 1030 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: 0.68 Conformation dependent library (CDL) restraints added in 284.9 milliseconds 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 380 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.890A pdb=" N GLY D 58 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A 58 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY E 58 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY I 58 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 60 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 67 through 70 removed outlier: 6.284A pdb=" N ASN A 67 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN E 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A 69 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 67 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 73 through 74 removed outlier: 6.412A pdb=" N VAL A 73 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL E 73 " --> pdb=" O ARG I 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 57 through 60 removed outlier: 6.389A pdb=" N GLY B 58 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY C 58 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY G 58 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY J 58 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 67 through 70 removed outlier: 6.283A pdb=" N ASN B 67 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN C 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 69 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN C 67 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN G 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 69 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN G 67 " --> pdb=" O ALA J 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 73 through 74 removed outlier: 6.409A pdb=" N VAL B 73 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 73 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL G 73 " --> pdb=" O ARG J 74 " (cutoff:3.500A) 23 hydrogen bonds defined for protein. 69 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: 0.37 Time building geometry restraints manager: 0.73 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: 580 1.34 - 1.46: 151 1.46 - 1.57: 919 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 1670 Sorted by residual: bond pdb=" N GLU I 60 " pdb=" CA GLU I 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.82e+00 bond pdb=" N GLU B 60 " pdb=" CA GLU B 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" N GLU A 60 " pdb=" CA GLU A 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N GLU D 60 " pdb=" CA GLU D 60 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N GLU E 60 " pdb=" CA GLU E 60 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.19e-02 7.06e+03 4.60e+00 ... (remaining 1665 not shown) Histogram of bond angle deviations from ideal: 100.83 - 106.54: 50 106.54 - 112.25: 752 112.25 - 117.96: 498 117.96 - 123.67: 870 123.67 - 129.37: 60 Bond angle restraints: 2230 Sorted by residual: angle pdb=" CA ASN E 70 " pdb=" C ASN E 70 " pdb=" O ASN E 70 " ideal model delta sigma weight residual 120.58 118.51 2.07 1.07e+00 8.73e-01 3.74e+00 angle pdb=" CA ASN H 70 " pdb=" C ASN H 70 " pdb=" O ASN H 70 " ideal model delta sigma weight residual 120.58 118.55 2.03 1.07e+00 8.73e-01 3.60e+00 angle pdb=" CA ASN D 70 " pdb=" C ASN D 70 " pdb=" O ASN D 70 " ideal model delta sigma weight residual 120.58 118.55 2.03 1.07e+00 8.73e-01 3.59e+00 angle pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" O ASN A 70 " ideal model delta sigma weight residual 120.58 118.56 2.02 1.07e+00 8.73e-01 3.57e+00 angle pdb=" CA ASN F 70 " pdb=" C ASN F 70 " pdb=" O ASN F 70 " ideal model delta sigma weight residual 120.58 118.59 1.99 1.07e+00 8.73e-01 3.47e+00 ... (remaining 2225 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.40: 940 13.40 - 26.79: 70 26.79 - 40.18: 0 40.18 - 53.57: 20 53.57 - 66.96: 20 Dihedral angle restraints: 1050 sinusoidal: 460 harmonic: 590 Sorted by residual: dihedral pdb=" CA GLU I 60 " pdb=" CB GLU I 60 " pdb=" CG GLU I 60 " pdb=" CD GLU I 60 " ideal model delta sinusoidal sigma weight residual 180.00 -131.06 -48.94 3 1.50e+01 4.44e-03 8.71e+00 dihedral pdb=" CA GLU G 60 " pdb=" CB GLU G 60 " pdb=" CG GLU G 60 " pdb=" CD GLU G 60 " ideal model delta sinusoidal sigma weight residual 180.00 -131.10 -48.90 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" CA GLU A 60 " pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " pdb=" CD GLU A 60 " ideal model delta sinusoidal sigma weight residual -180.00 -131.12 -48.88 3 1.50e+01 4.44e-03 8.70e+00 ... (remaining 1047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.031: 114 0.031 - 0.060: 53 0.060 - 0.090: 23 0.090 - 0.119: 40 0.119 - 0.148: 10 Chirality restraints: 240 Sorted by residual: chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA GLU E 60 " pdb=" N GLU E 60 " pdb=" C GLU E 60 " pdb=" CB GLU E 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA GLU H 60 " pdb=" N GLU H 60 " pdb=" C GLU H 60 " pdb=" CB GLU H 60 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 237 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 59 " -0.004 2.00e-02 2.50e+03 8.82e-03 7.78e-01 pdb=" C GLN D 59 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN D 59 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU D 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 59 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.77e-01 pdb=" C GLN E 59 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN E 59 " -0.006 2.00e-02 2.50e+03 pdb=" N GLU E 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 59 " 0.004 2.00e-02 2.50e+03 8.79e-03 7.72e-01 pdb=" C GLN F 59 " -0.015 2.00e-02 2.50e+03 pdb=" O GLN F 59 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU F 60 " 0.005 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 799 2.97 - 3.45: 1533 3.45 - 3.93: 2787 3.93 - 4.42: 2944 4.42 - 4.90: 5645 Nonbonded interactions: 13708 Sorted by model distance: nonbonded pdb=" N LYS A 61 " pdb=" O GLU E 60 " model vdw 2.486 2.520 nonbonded pdb=" N LYS C 61 " pdb=" O GLU G 60 " model vdw 2.492 2.520 nonbonded pdb=" O GLU B 60 " pdb=" N LYS F 61 " model vdw 2.492 2.520 nonbonded pdb=" N LYS B 61 " pdb=" O GLU C 60 " model vdw 2.492 2.520 nonbonded pdb=" O GLU A 60 " pdb=" N LYS D 61 " model vdw 2.498 2.520 ... (remaining 13703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.540 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: 11.680 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.130 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.005 0.031 1670 Z= 0.354 Angle : 0.637 4.375 2230 Z= 0.408 Chirality : 0.063 0.148 240 Planarity : 0.004 0.017 300 Dihedral : 16.255 66.959 670 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -3.75 (0.39), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.29), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 63 ARG 0.002 0.001 ARG I 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.209 Fit side-chains REVERT: B 64 GLN cc_start: 0.8667 (mt0) cc_final: 0.8403 (mt0) REVERT: J 74 ARG cc_start: 0.6515 (ttt-90) cc_final: 0.6254 (tpm170) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.2961 time to fit residues: 68.4878 Evaluate side-chains 48 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1670 Z= 0.247 Angle : 0.559 4.220 2230 Z= 0.298 Chirality : 0.057 0.136 240 Planarity : 0.003 0.020 300 Dihedral : 5.038 11.972 220 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 7.78 % Allowed : 11.11 % Favored : 81.11 % 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: -3.45 (0.44), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR B 63 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.213 Fit side-chains REVERT: D 55 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.4276 (tmt) REVERT: F 55 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.4531 (tmt) REVERT: G 60 GLU cc_start: 0.7683 (mp0) cc_final: 0.6240 (mp0) REVERT: H 55 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5001 (tmt) REVERT: H 67 ASN cc_start: 0.8864 (m-40) cc_final: 0.8651 (m110) REVERT: J 66 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7601 (mtmt) REVERT: J 74 ARG cc_start: 0.6902 (ttt-90) cc_final: 0.6612 (tpm170) outliers start: 14 outliers final: 3 residues processed: 63 average time/residue: 1.1634 time to fit residues: 74.4858 Evaluate side-chains 58 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.0270 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1670 Z= 0.192 Angle : 0.537 3.960 2230 Z= 0.289 Chirality : 0.058 0.128 240 Planarity : 0.003 0.018 300 Dihedral : 4.804 11.174 220 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 5.56 % Allowed : 16.11 % Favored : 78.33 % 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: -3.42 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 63 ARG 0.001 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.229 Fit side-chains REVERT: B 60 GLU cc_start: 0.7866 (mp0) cc_final: 0.6294 (mp0) REVERT: C 60 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7814 (mm-30) REVERT: G 60 GLU cc_start: 0.7631 (mp0) cc_final: 0.6207 (mp0) REVERT: H 55 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5046 (tmt) REVERT: H 67 ASN cc_start: 0.8896 (m-40) cc_final: 0.8684 (m110) REVERT: I 66 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7681 (mtmt) REVERT: J 66 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7649 (mtmt) REVERT: J 74 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6698 (tpm170) outliers start: 10 outliers final: 2 residues processed: 58 average time/residue: 1.3212 time to fit residues: 77.7740 Evaluate side-chains 55 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1670 Z= 0.181 Angle : 0.537 3.817 2230 Z= 0.288 Chirality : 0.058 0.126 240 Planarity : 0.003 0.029 300 Dihedral : 4.730 11.488 220 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.44 % Allowed : 20.00 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 63 ARG 0.000 0.000 ARG I 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.242 Fit side-chains REVERT: C 60 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7812 (mm-30) REVERT: H 55 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.4846 (tmt) REVERT: H 67 ASN cc_start: 0.8905 (m110) cc_final: 0.8699 (m110) REVERT: I 66 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: J 66 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7629 (mtmt) REVERT: J 74 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6726 (tpm170) outliers start: 8 outliers final: 1 residues processed: 52 average time/residue: 1.3118 time to fit residues: 69.1950 Evaluate side-chains 52 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.0070 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** 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: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1670 Z= 0.254 Angle : 0.574 4.762 2230 Z= 0.307 Chirality : 0.058 0.131 240 Planarity : 0.003 0.024 300 Dihedral : 4.943 11.885 220 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.00 % Allowed : 17.22 % Favored : 77.78 % 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: -3.28 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 63 ARG 0.001 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.221 Fit side-chains REVERT: C 60 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7849 (mm-30) REVERT: H 67 ASN cc_start: 0.8918 (m110) cc_final: 0.8714 (m110) REVERT: I 66 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7668 (mtmt) REVERT: J 60 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7997 (mm-30) outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 1.2865 time to fit residues: 75.7244 Evaluate side-chains 53 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.1052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1670 Z= 0.162 Angle : 0.551 3.959 2230 Z= 0.297 Chirality : 0.059 0.129 240 Planarity : 0.003 0.022 300 Dihedral : 4.688 12.001 220 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.22 % Allowed : 17.22 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR I 63 ARG 0.001 0.000 ARG I 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.218 Fit side-chains REVERT: A 60 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7558 (mm-30) REVERT: D 55 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.4786 (tmt) REVERT: F 55 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5062 (tmt) outliers start: 13 outliers final: 2 residues processed: 52 average time/residue: 1.3953 time to fit residues: 73.6089 Evaluate side-chains 51 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1670 Z= 0.187 Angle : 0.598 6.454 2230 Z= 0.320 Chirality : 0.059 0.128 240 Planarity : 0.002 0.018 300 Dihedral : 4.745 12.074 220 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.11 % Allowed : 19.44 % Favored : 74.44 % 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: -3.35 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR D 63 ARG 0.000 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.234 Fit side-chains REVERT: D 55 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.4802 (tmt) REVERT: F 55 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5120 (tmt) REVERT: J 66 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7655 (mtmt) outliers start: 11 outliers final: 2 residues processed: 48 average time/residue: 1.2756 time to fit residues: 62.2464 Evaluate side-chains 48 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.0050 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.0370 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1670 Z= 0.177 Angle : 0.547 4.965 2230 Z= 0.293 Chirality : 0.059 0.128 240 Planarity : 0.002 0.014 300 Dihedral : 4.707 11.740 220 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 5.00 % Allowed : 22.22 % Favored : 72.78 % 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: -3.27 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR I 63 ARG 0.001 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.279 Fit side-chains REVERT: D 55 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.4879 (tmt) REVERT: F 55 MET cc_start: 0.5881 (OUTLIER) cc_final: 0.5262 (tmm) REVERT: G 60 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7495 (mm-30) REVERT: J 66 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7643 (mtmt) outliers start: 9 outliers final: 1 residues processed: 48 average time/residue: 1.3622 time to fit residues: 66.5179 Evaluate side-chains 48 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1670 Z= 0.188 Angle : 0.575 5.543 2230 Z= 0.309 Chirality : 0.059 0.126 240 Planarity : 0.002 0.014 300 Dihedral : 4.752 11.782 220 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.44 % Allowed : 23.33 % Favored : 72.22 % 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: -3.26 (0.48), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR J 63 ARG 0.000 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.190 Fit side-chains REVERT: D 55 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4947 (tmm) REVERT: E 60 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7445 (mm-30) REVERT: F 55 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5319 (tmm) REVERT: J 66 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7625 (mtmt) outliers start: 8 outliers final: 1 residues processed: 45 average time/residue: 1.3706 time to fit residues: 62.6182 Evaluate side-chains 46 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain J residue 66 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.0000 chunk 4 optimal weight: 0.3980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1670 Z= 0.291 Angle : 0.596 5.677 2230 Z= 0.323 Chirality : 0.060 0.135 240 Planarity : 0.002 0.013 300 Dihedral : 5.101 12.100 220 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.33 % Allowed : 24.44 % Favored : 72.22 % 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: -3.21 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR J 63 ARG 0.001 0.000 ARG J 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.189 Fit side-chains REVERT: D 55 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5068 (tmm) REVERT: F 55 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5084 (tmt) REVERT: G 60 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7526 (mm-30) outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 1.2465 time to fit residues: 59.5529 Evaluate side-chains 47 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 55 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.0000 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.167004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.152437 restraints weight = 1766.336| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.07 r_work: 0.4482 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4356 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1670 Z= 0.204 Angle : 0.597 5.648 2230 Z= 0.323 Chirality : 0.060 0.133 240 Planarity : 0.002 0.012 300 Dihedral : 5.031 12.504 220 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.44 % Allowed : 26.11 % Favored : 69.44 % 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: -3.20 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR I 63 ARG 0.000 0.000 ARG J 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.99 seconds wall clock time: 34 minutes 31.71 seconds (2071.71 seconds total)