Starting phenix.real_space_refine on Mon Nov 13 15:11:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2023/8g2v_29682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2023/8g2v_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_29682/11_2023/8g2v_29682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2023/8g2v_29682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2023/8g2v_29682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2v_29682/11_2023/8g2v_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-1.21rc1-5144/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: 1.22, per 1000 atoms: 0.73 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: 0.65 Conformation dependent library (CDL) restraints added in 269.4 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: 0.26 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: 0.42 Time building geometry restraints manager: 0.72 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: 0.010 Normalize map: mean=0, sd=1: 2.370 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: 11.690 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.120 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:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.2513 time to fit residues: 66.1324 Evaluate side-chains 48 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2934 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 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: 0.7999 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1670 Z= 0.312 Angle : 0.590 4.572 2230 Z= 0.313 Chirality : 0.057 0.133 240 Planarity : 0.004 0.022 300 Dihedral : 5.164 12.812 220 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.22 % Allowed : 12.22 % Favored : 80.56 % 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: -3.43 (0.43), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.33), residues: 190 *********************** 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: 13 poor density : 58 time to evaluate : 0.217 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 64 average time/residue: 1.1377 time to fit residues: 74.0184 Evaluate side-chains 51 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.208 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN E 64 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN H 64 GLN H 67 ASN ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2910 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= 0.209 Angle : 0.585 4.050 2230 Z= 0.312 Chirality : 0.059 0.129 240 Planarity : 0.003 0.016 300 Dihedral : 4.916 10.853 220 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.44 % Allowed : 19.44 % Favored : 76.11 % 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: -3.36 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 190 *********************** 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 59 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.209 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 1.2973 time to fit residues: 75.0578 Evaluate side-chains 53 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 65 ASN ** 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: 0.7963 moved from start: 0.2995 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= 0.191 Angle : 0.551 3.900 2230 Z= 0.296 Chirality : 0.058 0.129 240 Planarity : 0.003 0.019 300 Dihedral : 4.839 11.902 220 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 21.11 % Favored : 76.11 % 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: -3.28 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.36), residues: 190 *********************** 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 55 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.219 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 1.0994 time to fit residues: 61.3884 Evaluate side-chains 51 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.154 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.0050 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 overall best weight: 0.4672 ------------------------------------------------------------------------------- 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 65 ASN ** 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: 0.7980 moved from start: 0.3116 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= 0.191 Angle : 0.542 4.597 2230 Z= 0.291 Chirality : 0.058 0.135 240 Planarity : 0.003 0.015 300 Dihedral : 4.733 12.107 220 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.89 % Allowed : 20.56 % 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: -3.32 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.36), residues: 190 *********************** 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 54 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.207 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 1.2745 time to fit residues: 65.9752 Evaluate side-chains 50 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.2148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 8 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1670 Z= 0.174 Angle : 0.581 5.676 2230 Z= 0.312 Chirality : 0.058 0.123 240 Planarity : 0.002 0.015 300 Dihedral : 4.704 12.466 220 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.89 % Allowed : 21.11 % Favored : 75.00 % 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: -3.44 (0.47), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.36), residues: 190 *********************** 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 56 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.192 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 1.2385 time to fit residues: 66.6805 Evaluate side-chains 49 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1670 Z= 0.280 Angle : 0.606 5.782 2230 Z= 0.325 Chirality : 0.060 0.139 240 Planarity : 0.003 0.029 300 Dihedral : 4.972 12.191 220 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.00 % Allowed : 21.11 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.36 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 190 *********************** 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 54 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.220 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 1.2875 time to fit residues: 65.4767 Evaluate side-chains 47 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.0270 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** 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: 0.8030 moved from start: 0.3459 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= 0.246 Angle : 0.629 6.225 2230 Z= 0.333 Chirality : 0.059 0.135 240 Planarity : 0.003 0.023 300 Dihedral : 4.992 11.729 220 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 24.44 % Favored : 73.33 % 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: -3.35 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 190 *********************** 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 48 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.205 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 1.1158 time to fit residues: 53.4162 Evaluate side-chains 46 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.205 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3547 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= 0.240 Angle : 0.643 5.736 2230 Z= 0.342 Chirality : 0.060 0.138 240 Planarity : 0.002 0.018 300 Dihedral : 5.050 12.470 220 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.67 % Allowed : 26.11 % 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: -3.32 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.35), residues: 190 *********************** 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 46 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.202 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 1.1215 time to fit residues: 52.5850 Evaluate side-chains 46 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.0040 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 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 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: 0.8020 moved from start: 0.3663 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= 0.225 Angle : 0.611 5.335 2230 Z= 0.327 Chirality : 0.060 0.135 240 Planarity : 0.002 0.019 300 Dihedral : 5.082 12.349 220 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.89 % Allowed : 24.44 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.29 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.35), residues: 190 ********************** 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 50 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.210 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 1.2710 time to fit residues: 60.7104 Evaluate side-chains 45 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.202 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.167533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.155243 restraints weight = 1810.321| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 1.88 r_work: 0.4492 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4375 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1670 Z= 0.238 Angle : 0.645 5.717 2230 Z= 0.345 Chirality : 0.060 0.135 240 Planarity : 0.002 0.019 300 Dihedral : 5.170 12.319 220 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.67 % Allowed : 27.22 % Favored : 71.11 % 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: -3.25 (0.46), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.80 seconds wall clock time: 34 minutes 30.96 seconds (2070.96 seconds total)