Starting phenix.real_space_refine on Mon Mar 11 13:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/03_2024/8ooa_17008.pdb" } resolution = 3.18 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 204 5.49 5 S 12 5.16 5 C 4638 2.51 5 N 1589 2.21 5 O 1962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8405 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2086 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "L" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2096 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "O" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "P" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "R" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 4.77, per 1000 atoms: 0.57 Number of scatterers: 8405 At special positions: 0 Unit cell: (114.258, 115.902, 77.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 204 15.00 O 1962 8.00 N 1589 7.00 C 4638 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: 4.55 Conformation dependent library (CDL) restraints added in 923.0 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 74.3% alpha, 3.0% beta 58 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'M' and resid 63 through 77 removed outlier: 4.267A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 113 removed outlier: 3.905A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.645A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 47 through 76 removed outlier: 4.178A pdb=" N TYR N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU N 52 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 34 through 43 Processing helix chain 'P' and resid 52 through 81 Processing helix chain 'P' and resid 87 through 99 Processing helix chain 'P' and resid 100 through 122 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.209A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.507A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.529A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.639A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.671A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.220A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.523A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.382A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 118 through 119 284 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 190 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 4.79 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: 1955 1.34 - 1.45: 2579 1.45 - 1.57: 4002 1.57 - 1.69: 409 1.69 - 1.81: 20 Bond restraints: 8965 Sorted by residual: bond pdb=" C4' DG L 63 " pdb=" C3' DG L 63 " ideal model delta sigma weight residual 1.523 1.577 -0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" C4' DG K 25 " pdb=" C3' DG K 25 " ideal model delta sigma weight residual 1.523 1.575 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C4' DG K 20 " pdb=" C3' DG K 20 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C4' DG L -5 " pdb=" C3' DG L -5 " ideal model delta sigma weight residual 1.523 1.571 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C4' DC K 4 " pdb=" C3' DC K 4 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.40: 1046 105.40 - 112.14: 4586 112.14 - 118.87: 2716 118.87 - 125.61: 3964 125.61 - 132.35: 659 Bond angle restraints: 12971 Sorted by residual: angle pdb=" O3' DC L -25 " pdb=" P DT L -24 " pdb=" O5' DT L -24 " ideal model delta sigma weight residual 104.00 99.62 4.38 1.50e+00 4.44e-01 8.54e+00 angle pdb=" C4' DC K 21 " pdb=" O4' DC K 21 " pdb=" C1' DC K 21 " ideal model delta sigma weight residual 109.70 105.34 4.36 1.50e+00 4.44e-01 8.45e+00 angle pdb=" O3' DG L 27 " pdb=" P DA L 28 " pdb=" O5' DA L 28 " ideal model delta sigma weight residual 104.00 99.89 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" O3' DC L -28 " pdb=" P DC L -27 " pdb=" O5' DC L -27 " ideal model delta sigma weight residual 104.00 99.93 4.07 1.50e+00 4.44e-01 7.35e+00 angle pdb=" O3' DA K -45 " pdb=" P DA K -44 " pdb=" O5' DA K -44 " ideal model delta sigma weight residual 104.00 100.01 3.99 1.50e+00 4.44e-01 7.09e+00 ... (remaining 12966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3198 17.66 - 35.31: 630 35.31 - 52.97: 794 52.97 - 70.62: 212 70.62 - 88.28: 25 Dihedral angle restraints: 4859 sinusoidal: 3327 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ILE M 112 " pdb=" C ILE M 112 " pdb=" N HIS M 113 " pdb=" CA HIS M 113 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA ASP Q 81 " pdb=" C ASP Q 81 " pdb=" N LEU Q 82 " pdb=" CA LEU Q 82 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLY N 28 " pdb=" C GLY N 28 " pdb=" N ILE N 29 " pdb=" CA ILE N 29 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 741 0.039 - 0.079: 516 0.079 - 0.118: 156 0.118 - 0.157: 51 0.157 - 0.196: 11 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CB ILE N 29 " pdb=" CA ILE N 29 " pdb=" CG1 ILE N 29 " pdb=" CG2 ILE N 29 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" C1' DT L 15 " pdb=" O4' DT L 15 " pdb=" C2' DT L 15 " pdb=" N1 DT L 15 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA ILE O 79 " pdb=" N ILE O 79 " pdb=" C ILE O 79 " pdb=" CB ILE O 79 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1472 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 92 " -0.324 9.50e-02 1.11e+02 1.46e-01 1.58e+01 pdb=" NE ARG N 92 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG N 92 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG N 92 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG N 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " 0.003 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR Q 41 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 83 " -0.240 9.50e-02 1.11e+02 1.08e-01 8.70e+00 pdb=" NE ARG M 83 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG M 83 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG M 83 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG M 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1742 2.82 - 3.34: 7553 3.34 - 3.86: 16370 3.86 - 4.38: 20627 4.38 - 4.90: 28006 Nonbonded interactions: 74298 Sorted by model distance: nonbonded pdb=" OH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 2.299 2.440 nonbonded pdb=" OD2 ASP M 106 " pdb=" NH1 ARG M 131 " model vdw 2.377 2.520 nonbonded pdb=" OP1 DG L 8 " pdb=" N ILE N 46 " model vdw 2.398 2.520 nonbonded pdb=" OP1 DA L 28 " pdb=" N LYS N 79 " model vdw 2.412 2.520 nonbonded pdb=" OD2 ASP P 65 " pdb=" OH TYR R 98 " model vdw 2.425 2.440 ... (remaining 74293 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 'N' and resid 23 through 95) selection = (chain 'R' and resid 23 through 95) } 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=0.00 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.740 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.560 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.008 0.057 8965 Z= 0.404 Angle : 1.083 4.754 12971 Z= 0.589 Chirality : 0.057 0.196 1475 Planarity : 0.012 0.146 936 Dihedral : 27.962 88.276 3869 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.30), residues: 517 helix: -1.41 (0.21), residues: 388 sheet: None (None), residues: 0 loop : -0.64 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.026 0.002 PHE R 100 TYR 0.035 0.006 TYR Q 41 ARG 0.029 0.004 ARG N 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: N 57 VAL cc_start: 0.8072 (t) cc_final: 0.7789 (m) REVERT: N 91 LYS cc_start: 0.8304 (mttt) cc_final: 0.7853 (mtpt) REVERT: O 74 LYS cc_start: 0.7891 (mttt) cc_final: 0.7667 (mptt) REVERT: P 32 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5638 (pt0) REVERT: P 44 GLN cc_start: 0.7192 (mt0) cc_final: 0.6991 (mt0) REVERT: Q 58 THR cc_start: 0.7089 (p) cc_final: 0.6852 (p) REVERT: Q 64 LYS cc_start: 0.7827 (mttt) cc_final: 0.7426 (mtpt) REVERT: Q 68 GLN cc_start: 0.8021 (mt0) cc_final: 0.7814 (mt0) REVERT: R 25 ASN cc_start: 0.7507 (m-40) cc_final: 0.7123 (m110) REVERT: R 57 VAL cc_start: 0.8440 (t) cc_final: 0.8096 (m) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3933 time to fit residues: 57.3735 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 0.0270 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 125 GLN O 104 GLN P 60 ASN P 64 ASN P 79 HIS P 81 ASN Q 108 ASN R 75 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8965 Z= 0.199 Angle : 0.591 4.977 12971 Z= 0.356 Chirality : 0.036 0.137 1475 Planarity : 0.004 0.033 936 Dihedral : 32.264 91.224 2801 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.35 % Allowed : 6.32 % Favored : 92.33 % 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: 1.34 (0.35), residues: 517 helix: 1.30 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.16 (0.46), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS R 75 PHE 0.017 0.002 PHE P 62 TYR 0.023 0.002 TYR N 88 ARG 0.003 0.000 ARG P 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: M 118 THR cc_start: 0.7089 (m) cc_final: 0.6819 (p) REVERT: N 91 LYS cc_start: 0.7965 (mttt) cc_final: 0.7214 (mmtt) REVERT: P 68 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6808 (mt-10) REVERT: Q 58 THR cc_start: 0.7134 (p) cc_final: 0.6733 (p) REVERT: Q 109 LEU cc_start: 0.8356 (mt) cc_final: 0.8099 (mm) REVERT: R 25 ASN cc_start: 0.7594 (m-40) cc_final: 0.7235 (m110) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.3597 time to fit residues: 42.4447 Evaluate side-chains 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 106 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN P 64 ASN Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8965 Z= 0.232 Angle : 0.591 4.995 12971 Z= 0.353 Chirality : 0.036 0.138 1475 Planarity : 0.005 0.033 936 Dihedral : 31.587 89.497 2801 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.35 % Allowed : 8.13 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 517 helix: 1.53 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.08 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.013 0.002 PHE P 62 TYR 0.019 0.002 TYR N 88 ARG 0.011 0.001 ARG O 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.597 Fit side-chains REVERT: N 91 LYS cc_start: 0.8050 (mttt) cc_final: 0.7797 (mtpt) REVERT: O 74 LYS cc_start: 0.7554 (mptt) cc_final: 0.7328 (mppt) REVERT: P 69 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: Q 64 LYS cc_start: 0.7407 (mtmt) cc_final: 0.6894 (mtpt) REVERT: R 25 ASN cc_start: 0.7696 (m-40) cc_final: 0.7259 (m110) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.3432 time to fit residues: 38.5851 Evaluate side-chains 85 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8965 Z= 0.188 Angle : 0.546 4.800 12971 Z= 0.330 Chirality : 0.034 0.137 1475 Planarity : 0.004 0.031 936 Dihedral : 31.342 93.380 2801 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.35 % Allowed : 10.84 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.36), residues: 517 helix: 2.00 (0.26), residues: 387 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.013 0.002 PHE P 62 TYR 0.018 0.002 TYR N 88 ARG 0.002 0.000 ARG Q 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.688 Fit side-chains REVERT: N 91 LYS cc_start: 0.8034 (mttt) cc_final: 0.7780 (mtpt) REVERT: O 95 LYS cc_start: 0.8317 (tptm) cc_final: 0.8085 (tptp) REVERT: P 69 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7251 (ttm170) REVERT: Q 64 LYS cc_start: 0.7333 (mttt) cc_final: 0.6860 (mtpt) REVERT: R 25 ASN cc_start: 0.7730 (m-40) cc_final: 0.7278 (m110) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.3506 time to fit residues: 35.6280 Evaluate side-chains 82 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8965 Z= 0.237 Angle : 0.578 5.734 12971 Z= 0.346 Chirality : 0.036 0.149 1475 Planarity : 0.004 0.032 936 Dihedral : 31.346 90.398 2801 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 10.38 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.36), residues: 517 helix: 1.79 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.02 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.010 0.002 PHE R 100 TYR 0.021 0.002 TYR N 88 ARG 0.003 0.000 ARG P 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.583 Fit side-chains REVERT: N 91 LYS cc_start: 0.8111 (mttt) cc_final: 0.7810 (mtpt) REVERT: P 69 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7410 (ttm170) REVERT: Q 64 LYS cc_start: 0.7458 (mttt) cc_final: 0.6943 (mtpt) REVERT: R 25 ASN cc_start: 0.7723 (m-40) cc_final: 0.7277 (m110) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.3259 time to fit residues: 35.6479 Evaluate side-chains 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN P 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8965 Z= 0.247 Angle : 0.585 5.128 12971 Z= 0.349 Chirality : 0.036 0.149 1475 Planarity : 0.005 0.033 936 Dihedral : 31.156 89.438 2801 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 11.96 % Favored : 85.78 % 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: 1.85 (0.36), residues: 517 helix: 1.68 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.05 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.009 0.002 PHE M 67 TYR 0.021 0.002 TYR N 88 ARG 0.004 0.000 ARG Q 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.648 Fit side-chains REVERT: N 88 TYR cc_start: 0.7513 (m-80) cc_final: 0.7210 (m-80) REVERT: N 91 LYS cc_start: 0.8154 (mttt) cc_final: 0.7826 (mtpt) REVERT: P 69 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7460 (ttm170) REVERT: R 25 ASN cc_start: 0.7710 (m-40) cc_final: 0.7248 (m110) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.3347 time to fit residues: 36.1305 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8965 Z= 0.203 Angle : 0.567 5.035 12971 Z= 0.342 Chirality : 0.035 0.148 1475 Planarity : 0.004 0.033 936 Dihedral : 31.139 90.125 2801 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.16 % Allowed : 11.51 % Favored : 85.33 % 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: 2.04 (0.36), residues: 517 helix: 1.84 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.05 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.013 0.002 PHE R 100 TYR 0.016 0.002 TYR N 88 ARG 0.002 0.000 ARG M 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.653 Fit side-chains REVERT: N 91 LYS cc_start: 0.8125 (mttt) cc_final: 0.7810 (mtpt) REVERT: P 69 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7346 (ttm170) REVERT: R 25 ASN cc_start: 0.7701 (m-40) cc_final: 0.7249 (m110) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.3375 time to fit residues: 36.7689 Evaluate side-chains 91 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 61 optimal weight: 0.0000 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8965 Z= 0.175 Angle : 0.551 6.515 12971 Z= 0.334 Chirality : 0.034 0.137 1475 Planarity : 0.004 0.033 936 Dihedral : 31.067 92.091 2801 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 12.64 % Favored : 85.33 % 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: 2.30 (0.36), residues: 517 helix: 2.04 (0.26), residues: 388 sheet: None (None), residues: 0 loop : 0.01 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 75 PHE 0.011 0.002 PHE P 62 TYR 0.029 0.002 TYR N 88 ARG 0.004 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.601 Fit side-chains REVERT: N 91 LYS cc_start: 0.8089 (mttt) cc_final: 0.7776 (mtpt) REVERT: O 95 LYS cc_start: 0.8334 (tptm) cc_final: 0.8121 (tptp) REVERT: P 69 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7257 (ttm170) REVERT: R 25 ASN cc_start: 0.7697 (m-40) cc_final: 0.7239 (m110) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.3559 time to fit residues: 35.8241 Evaluate side-chains 87 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8965 Z= 0.196 Angle : 0.551 5.683 12971 Z= 0.333 Chirality : 0.034 0.136 1475 Planarity : 0.004 0.032 936 Dihedral : 30.979 93.391 2801 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 12.42 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.36), residues: 517 helix: 2.05 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.02 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.009 0.002 PHE R 100 TYR 0.025 0.002 TYR N 88 ARG 0.003 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.630 Fit side-chains REVERT: N 91 LYS cc_start: 0.8122 (mttt) cc_final: 0.7808 (mtpt) REVERT: O 95 LYS cc_start: 0.8355 (tptm) cc_final: 0.8134 (tptp) REVERT: P 69 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: R 25 ASN cc_start: 0.7704 (m-40) cc_final: 0.7268 (m110) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.3485 time to fit residues: 35.5568 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.0000 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8965 Z= 0.194 Angle : 0.548 5.744 12971 Z= 0.332 Chirality : 0.034 0.138 1475 Planarity : 0.004 0.032 936 Dihedral : 30.973 93.469 2801 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.36), residues: 517 helix: 2.07 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.01 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 75 PHE 0.009 0.002 PHE Q 67 TYR 0.019 0.002 TYR N 88 ARG 0.003 0.000 ARG R 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.661 Fit side-chains REVERT: N 91 LYS cc_start: 0.8127 (mttt) cc_final: 0.7812 (mtpt) REVERT: O 95 LYS cc_start: 0.8355 (tptm) cc_final: 0.8135 (tptp) REVERT: P 69 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7297 (ttm170) REVERT: R 25 ASN cc_start: 0.7703 (m-40) cc_final: 0.7265 (m110) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.3581 time to fit residues: 37.1068 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108715 restraints weight = 11056.732| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 0.64 r_work: 0.3329 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8965 Z= 0.228 Angle : 0.569 6.075 12971 Z= 0.341 Chirality : 0.035 0.146 1475 Planarity : 0.004 0.032 936 Dihedral : 30.979 91.609 2801 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.36), residues: 517 helix: 1.95 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.010 0.002 PHE R 100 TYR 0.019 0.002 TYR N 88 ARG 0.003 0.000 ARG R 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.32 seconds wall clock time: 35 minutes 47.47 seconds (2147.47 seconds total)