Starting phenix.real_space_refine on Sat Dec 9 18:37:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g86_29837/12_2023/8g86_29837.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 290 5.49 5 S 12 5.16 5 C 6637 2.51 5 N 2229 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11972 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2995 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 6.40, per 1000 atoms: 0.53 Number of scatterers: 11972 At special positions: 0 Unit cell: (74.865, 116.725, 114.31, 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 290 15.00 O 2804 8.00 N 2229 7.00 C 6637 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: 5.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.4% alpha, 2.9% beta 134 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.145A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.236A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.829A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.387A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.003A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.691A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.769A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.764A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.057A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 417 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 634 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2227 1.33 - 1.45: 4184 1.45 - 1.57: 5764 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12775 Sorted by residual: bond pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" C3' DT J 41 " pdb=" C2' DT J 41 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.20e-01 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.07e-01 bond pdb=" C3' DC I -22 " pdb=" C2' DC I -22 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.00e-01 bond pdb=" C3' DG I 68 " pdb=" C2' DG I 68 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.94e-01 ... (remaining 12770 not shown) Histogram of bond angle deviations from ideal: 99.20 - 105.84: 1543 105.84 - 112.49: 6920 112.49 - 119.14: 3282 119.14 - 125.79: 5765 125.79 - 132.44: 988 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 118.43 -5.25 2.37e+00 1.78e-01 4.91e+00 angle pdb=" CA LEU F 22 " pdb=" CB LEU F 22 " pdb=" CG LEU F 22 " ideal model delta sigma weight residual 116.30 123.36 -7.06 3.50e+00 8.16e-02 4.07e+00 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 117.81 -4.63 2.37e+00 1.78e-01 3.82e+00 angle pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " pdb=" C1' DA I 29 " ideal model delta sigma weight residual 101.60 104.30 -2.70 1.50e+00 4.44e-01 3.24e+00 angle pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 122.87 -2.67 1.50e+00 4.44e-01 3.17e+00 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 5664 35.88 - 71.77: 1344 71.77 - 107.65: 13 107.65 - 143.53: 0 143.53 - 179.41: 1 Dihedral angle restraints: 7022 sinusoidal: 4817 harmonic: 2205 Sorted by residual: dihedral pdb=" C4' DT I 20 " pdb=" C3' DT I 20 " pdb=" O3' DT I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.41 -179.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU F 74 " pdb=" CG GLU F 74 " pdb=" CD GLU F 74 " pdb=" OE1 GLU F 74 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1457 0.026 - 0.052: 505 0.052 - 0.078: 103 0.078 - 0.104: 24 0.104 - 0.130: 20 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2106 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO G 80 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 80 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 66 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.019 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2611 2.81 - 3.33: 10262 3.33 - 3.85: 24101 3.85 - 4.38: 30291 4.38 - 4.90: 40295 Nonbonded interactions: 107560 Sorted by model distance: nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.287 2.440 nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DT J -23 " model vdw 2.328 2.520 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DC I -42 " model vdw 2.386 2.520 nonbonded pdb=" O2 DC I -42 " pdb=" N2 DG J 42 " model vdw 2.395 2.520 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.425 2.496 ... (remaining 107555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.210 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: 14.630 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.340 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.003 0.038 12775 Z= 0.178 Angle : 0.502 7.065 18498 Z= 0.305 Chirality : 0.029 0.130 2109 Planarity : 0.003 0.047 1335 Dihedral : 27.264 179.413 5598 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.95 % Allowed : 16.30 % Favored : 82.75 % 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: 1.60 (0.28), residues: 743 helix: 1.47 (0.20), residues: 551 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.992 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 163 average time/residue: 1.9486 time to fit residues: 334.0230 Evaluate side-chains 140 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12775 Z= 0.250 Angle : 0.599 7.633 18498 Z= 0.362 Chirality : 0.035 0.123 2109 Planarity : 0.005 0.043 1335 Dihedral : 30.602 178.364 4095 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.64 % Allowed : 16.30 % Favored : 80.06 % 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: 2.58 (0.29), residues: 743 helix: 2.29 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.002 TYR B 51 ARG 0.006 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 0.976 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 166 average time/residue: 1.9889 time to fit residues: 347.1092 Evaluate side-chains 155 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.9779 time to fit residues: 5.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12775 Z= 0.374 Angle : 0.663 7.663 18498 Z= 0.393 Chirality : 0.040 0.162 2109 Planarity : 0.006 0.084 1335 Dihedral : 31.058 176.317 4095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.27 % Allowed : 15.35 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 743 helix: 2.14 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.015 0.002 PHE A 67 TYR 0.015 0.002 TYR E 54 ARG 0.010 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.910 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 152 average time/residue: 2.0563 time to fit residues: 328.1777 Evaluate side-chains 151 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 1.0897 time to fit residues: 6.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 0.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12775 Z= 0.226 Angle : 0.591 7.150 18498 Z= 0.358 Chirality : 0.035 0.130 2109 Planarity : 0.004 0.044 1335 Dihedral : 30.928 177.018 4095 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.69 % Allowed : 17.56 % Favored : 79.75 % 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: 2.63 (0.29), residues: 743 helix: 2.37 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.014 0.001 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.002 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.167 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 153 average time/residue: 2.0217 time to fit residues: 325.3876 Evaluate side-chains 151 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.9858 time to fit residues: 5.2991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12775 Z= 0.198 Angle : 0.550 6.825 18498 Z= 0.335 Chirality : 0.032 0.129 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.294 179.514 4095 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.22 % Allowed : 17.88 % Favored : 79.91 % 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: 2.96 (0.29), residues: 743 helix: 2.66 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.005 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 0.989 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 157 average time/residue: 1.9482 time to fit residues: 322.2242 Evaluate side-chains 156 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.6734 time to fit residues: 4.6040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12775 Z= 0.273 Angle : 0.595 7.367 18498 Z= 0.357 Chirality : 0.035 0.132 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.603 176.838 4095 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.22 % Allowed : 18.51 % Favored : 79.27 % 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: 2.70 (0.29), residues: 743 helix: 2.43 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.004 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 0.839 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 1.9482 time to fit residues: 317.8569 Evaluate side-chains 155 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.2788 time to fit residues: 6.5766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12775 Z= 0.207 Angle : 0.576 7.557 18498 Z= 0.347 Chirality : 0.033 0.131 2109 Planarity : 0.004 0.040 1335 Dihedral : 30.599 177.126 4095 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.01 % Allowed : 17.56 % Favored : 79.43 % 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: 2.80 (0.29), residues: 743 helix: 2.51 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.007 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.850 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 1.9576 time to fit residues: 319.5811 Evaluate side-chains 157 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.5714 time to fit residues: 8.2899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 12775 Z= 0.540 Angle : 0.771 8.055 18498 Z= 0.448 Chirality : 0.048 0.220 2109 Planarity : 0.006 0.045 1335 Dihedral : 31.650 174.140 4095 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.48 % Allowed : 16.93 % Favored : 79.59 % 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: 2.05 (0.29), residues: 743 helix: 1.96 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 75 PHE 0.019 0.003 PHE C 25 TYR 0.017 0.003 TYR E 54 ARG 0.008 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.979 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 145 average time/residue: 2.1659 time to fit residues: 329.8877 Evaluate side-chains 147 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.2588 time to fit residues: 6.4451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12775 Z= 0.223 Angle : 0.582 7.439 18498 Z= 0.352 Chirality : 0.034 0.129 2109 Planarity : 0.004 0.044 1335 Dihedral : 30.819 178.134 4095 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.74 % Allowed : 18.67 % Favored : 79.59 % 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: 2.66 (0.29), residues: 743 helix: 2.43 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.010 0.002 TYR H 37 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.998 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 2.0382 time to fit residues: 325.9742 Evaluate side-chains 150 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7050 time to fit residues: 2.8832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12775 Z= 0.236 Angle : 0.585 7.341 18498 Z= 0.352 Chirality : 0.034 0.131 2109 Planarity : 0.004 0.042 1335 Dihedral : 30.748 177.178 4095 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.22 % Allowed : 18.67 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.29), residues: 743 helix: 2.46 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.005 0.000 ARG A 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.992 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 153 average time/residue: 1.9927 time to fit residues: 320.8037 Evaluate side-chains 151 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.6700 time to fit residues: 4.5831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 44 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134406 restraints weight = 10588.892| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 0.91 r_work: 0.3373 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12775 Z= 0.250 Angle : 0.590 7.373 18498 Z= 0.354 Chirality : 0.035 0.133 2109 Planarity : 0.004 0.043 1335 Dihedral : 30.734 176.595 4095 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.06 % Allowed : 18.67 % Favored : 79.27 % 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: 2.67 (0.29), residues: 743 helix: 2.42 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.011 0.002 TYR B 51 ARG 0.004 0.000 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5258.57 seconds wall clock time: 93 minutes 19.73 seconds (5599.73 seconds total)