Starting phenix.real_space_refine on Tue Sep 24 13:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/09_2024/8ooa_17008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/09_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_17008/09_2024/8ooa_17008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/09_2024/8ooa_17008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/09_2024/8ooa_17008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooa_17008/09_2024/8ooa_17008.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.51, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 895.1 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: 2.85 Time building geometry restraints manager: 2.40 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: 0.00 - 0.95: 9801 0.95 - 1.90: 1946 1.90 - 2.85: 705 2.85 - 3.80: 470 3.80 - 4.75: 49 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 3.040 nonbonded pdb=" OD2 ASP M 106 " pdb=" NH1 ARG M 131 " model vdw 2.377 3.120 nonbonded pdb=" OP1 DG L 8 " pdb=" N ILE N 46 " model vdw 2.398 3.120 nonbonded pdb=" OP1 DA L 28 " pdb=" N LYS N 79 " model vdw 2.412 3.120 nonbonded pdb=" OD2 ASP P 65 " pdb=" OH TYR R 98 " model vdw 2.425 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 4.070 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.180 Find NCS groups from input model: 0.140 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 : 0.608 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: 0.3902 time to fit residues: 56.9158 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 0.0010 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 R 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8965 Z= 0.215 Angle : 0.590 4.828 12971 Z= 0.357 Chirality : 0.036 0.134 1475 Planarity : 0.004 0.032 936 Dihedral : 32.273 90.757 2801 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.68 % Allowed : 6.55 % Favored : 92.78 % 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: 1.20 (0.35), residues: 517 helix: 1.20 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.19 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS R 75 PHE 0.016 0.002 PHE P 62 TYR 0.019 0.002 TYR N 88 ARG 0.006 0.000 ARG P 76 *********************** 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 99 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: N 91 LYS cc_start: 0.7933 (mttt) cc_final: 0.7177 (mmtt) REVERT: N 92 ARG cc_start: 0.7189 (mtp85) cc_final: 0.6946 (mtp85) REVERT: O 90 ASP cc_start: 0.7734 (t70) cc_final: 0.7444 (t70) REVERT: P 32 GLU cc_start: 0.5917 (mt-10) cc_final: 0.5675 (pt0) REVERT: P 68 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6794 (mt-10) REVERT: P 82 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7402 (mttp) REVERT: Q 53 ARG cc_start: 0.7543 (ttm170) cc_final: 0.7318 (ttp-170) REVERT: Q 58 THR cc_start: 0.7202 (p) cc_final: 0.6820 (p) REVERT: Q 109 LEU cc_start: 0.8350 (mt) cc_final: 0.8087 (mm) REVERT: R 25 ASN cc_start: 0.7673 (m-40) cc_final: 0.7298 (m110) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.3551 time to fit residues: 41.6329 Evaluate side-chains 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU 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: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7242 moved from start: 0.3220 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= 0.206 Angle : 0.569 4.917 12971 Z= 0.343 Chirality : 0.035 0.139 1475 Planarity : 0.004 0.031 936 Dihedral : 31.546 90.059 2801 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.90 % Allowed : 8.13 % Favored : 90.97 % 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: 1.79 (0.35), residues: 517 helix: 1.66 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.16 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.016 0.002 PHE P 62 TYR 0.018 0.002 TYR N 88 ARG 0.006 0.001 ARG R 55 *********************** 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 97 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.643 Fit side-chains REVERT: N 91 LYS cc_start: 0.7984 (mttt) cc_final: 0.7739 (mtpt) REVERT: N 92 ARG cc_start: 0.7161 (mtp85) cc_final: 0.6893 (mtp85) REVERT: P 32 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5540 (pt0) REVERT: P 68 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6835 (mt-10) REVERT: Q 64 LYS cc_start: 0.7360 (mtmt) cc_final: 0.6872 (mtpt) REVERT: Q 73 GLU cc_start: 0.7790 (tt0) cc_final: 0.7497 (tt0) REVERT: R 25 ASN cc_start: 0.7714 (m-40) cc_final: 0.7313 (m110) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.3322 time to fit residues: 38.2648 Evaluate side-chains 82 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 64 GLU 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: 1.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3586 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= 0.205 Angle : 0.557 4.808 12971 Z= 0.335 Chirality : 0.035 0.143 1475 Planarity : 0.004 0.032 936 Dihedral : 31.223 91.228 2801 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.90 % Allowed : 11.74 % 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: 2.08 (0.36), residues: 517 helix: 1.87 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -0.00 (0.50), residues: 130 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 0.018 0.002 TYR N 88 ARG 0.004 0.000 ARG Q 128 *********************** 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 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.619 Fit side-chains REVERT: N 91 LYS cc_start: 0.8011 (mttt) cc_final: 0.7738 (mtpt) REVERT: N 92 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6879 (mtp85) REVERT: P 32 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5553 (pt0) REVERT: P 68 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6776 (mt-10) REVERT: P 82 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7404 (mttm) REVERT: Q 64 LYS cc_start: 0.7320 (mttt) cc_final: 0.6846 (mtpt) outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.3550 time to fit residues: 37.2154 Evaluate side-chains 83 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain P residue 53 SER 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: 0.6980 chunk 27 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN O 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3658 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= 0.183 Angle : 0.541 4.917 12971 Z= 0.328 Chirality : 0.034 0.144 1475 Planarity : 0.004 0.033 936 Dihedral : 31.145 91.733 2801 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.81 % Allowed : 10.61 % Favored : 87.58 % 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: 387 sheet: None (None), residues: 0 loop : -0.01 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 75 PHE 0.011 0.002 PHE R 100 TYR 0.028 0.002 TYR N 88 ARG 0.002 0.000 ARG R 92 *********************** 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 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.638 Fit side-chains REVERT: N 91 LYS cc_start: 0.8045 (mttt) cc_final: 0.7756 (mtpt) REVERT: N 92 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6888 (mtp85) REVERT: P 32 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5519 (pt0) REVERT: P 82 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7466 (mttm) REVERT: Q 64 LYS cc_start: 0.7284 (mttt) cc_final: 0.6818 (mtpt) REVERT: Q 73 GLU cc_start: 0.7745 (tt0) cc_final: 0.7492 (tt0) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.3331 time to fit residues: 34.0876 Evaluate side-chains 84 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 57 SER 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: 0.8980 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8965 Z= 0.276 Angle : 0.603 5.061 12971 Z= 0.360 Chirality : 0.037 0.146 1475 Planarity : 0.005 0.035 936 Dihedral : 31.415 87.309 2801 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.58 % Allowed : 12.42 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.35), residues: 517 helix: 1.63 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.22 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.012 0.002 PHE R 100 TYR 0.021 0.002 TYR N 88 ARG 0.003 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 93 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.729 Fit side-chains REVERT: N 92 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6897 (mtp85) REVERT: P 32 GLU cc_start: 0.5764 (mt-10) cc_final: 0.5513 (pt0) REVERT: P 82 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7448 (mttm) REVERT: Q 64 LYS cc_start: 0.7450 (mttt) cc_final: 0.6955 (mtpt) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.3958 time to fit residues: 44.2057 Evaluate side-chains 91 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN O 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3748 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= 0.205 Angle : 0.575 6.804 12971 Z= 0.347 Chirality : 0.035 0.190 1475 Planarity : 0.004 0.034 936 Dihedral : 31.362 88.981 2801 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.03 % Allowed : 12.19 % 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: 1.98 (0.36), residues: 517 helix: 1.83 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.17 (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 0.031 0.002 TYR P 80 ARG 0.002 0.000 ARG M 83 *********************** 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 94 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.659 Fit side-chains REVERT: N 92 ARG cc_start: 0.7170 (mtp85) cc_final: 0.6870 (mtp85) REVERT: P 32 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5511 (pt0) REVERT: P 82 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7454 (mttm) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.3607 time to fit residues: 40.0777 Evaluate side-chains 91 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 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 O residue 104 GLN 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 71 VAL 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: 0.7980 chunk 45 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8965 Z= 0.188 Angle : 0.556 6.060 12971 Z= 0.336 Chirality : 0.034 0.176 1475 Planarity : 0.004 0.033 936 Dihedral : 31.212 91.392 2801 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.90 % Allowed : 14.00 % 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: 2.20 (0.36), residues: 517 helix: 2.00 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.13 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 75 PHE 0.010 0.002 PHE P 67 TYR 0.020 0.002 TYR N 88 ARG 0.002 0.000 ARG M 129 *********************** 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 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.662 Fit side-chains REVERT: N 92 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6862 (mtp85) REVERT: O 36 LYS cc_start: 0.8050 (mptt) cc_final: 0.7721 (mttp) REVERT: O 102 ILE cc_start: 0.8469 (mt) cc_final: 0.8251 (mp) REVERT: P 32 GLU cc_start: 0.5771 (mt-10) cc_final: 0.5518 (pt0) REVERT: P 82 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7438 (mttm) outliers start: 4 outliers final: 4 residues processed: 87 average time/residue: 0.3513 time to fit residues: 37.2665 Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain P residue 98 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN O 104 GLN R 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8965 Z= 0.236 Angle : 0.575 5.995 12971 Z= 0.345 Chirality : 0.035 0.160 1475 Planarity : 0.004 0.033 936 Dihedral : 31.092 89.630 2801 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.26 % Allowed : 12.64 % 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: 2.04 (0.36), residues: 517 helix: 1.87 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.13 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 75 PHE 0.010 0.002 PHE R 100 TYR 0.017 0.002 TYR N 88 ARG 0.002 0.000 ARG M 129 *********************** 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 91 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.648 Fit side-chains REVERT: N 92 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6876 (mtp85) REVERT: O 36 LYS cc_start: 0.8086 (mptt) cc_final: 0.7752 (mttp) REVERT: P 32 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5531 (pt0) REVERT: P 82 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7447 (mttm) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.3346 time to fit residues: 36.2677 Evaluate side-chains 88 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain P residue 53 SER 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 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8965 Z= 0.231 Angle : 0.574 6.928 12971 Z= 0.344 Chirality : 0.035 0.204 1475 Planarity : 0.004 0.034 936 Dihedral : 31.081 90.237 2801 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.81 % Allowed : 13.09 % 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: 2.04 (0.36), residues: 517 helix: 1.87 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.13 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.011 0.002 PHE R 100 TYR 0.014 0.002 TYR N 88 ARG 0.002 0.000 ARG M 129 ********************** 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 90 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.660 Fit side-chains REVERT: N 92 ARG cc_start: 0.7175 (mtp85) cc_final: 0.6887 (mtp85) REVERT: O 36 LYS cc_start: 0.8089 (mptt) cc_final: 0.7752 (mttp) REVERT: P 32 GLU cc_start: 0.5790 (mt-10) cc_final: 0.5513 (pt0) REVERT: P 82 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7445 (mttm) outliers start: 8 outliers final: 8 residues processed: 88 average time/residue: 0.3409 time to fit residues: 36.7545 Evaluate side-chains 89 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain P residue 53 SER 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 71 VAL 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: 0.9980 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109018 restraints weight = 11060.724| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.65 r_work: 0.3331 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8965 Z= 0.237 Angle : 0.575 6.798 12971 Z= 0.344 Chirality : 0.035 0.167 1475 Planarity : 0.004 0.035 936 Dihedral : 30.885 91.162 2801 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.03 % Allowed : 13.09 % Favored : 84.88 % 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: 2.02 (0.36), residues: 517 helix: 1.83 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -0.09 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 75 PHE 0.012 0.002 PHE R 100 TYR 0.014 0.002 TYR N 88 ARG 0.003 0.000 ARG M 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.52 seconds wall clock time: 36 minutes 25.01 seconds (2185.01 seconds total)