Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:33:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6riu_4898/04_2022/6riu_4898.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 2882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Time building chain proxies: 1.88, per 1000 atoms: 0.65 Number of scatterers: 2882 At special positions: 0 Unit cell: (69.828, 47.61, 49.726, 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 4 16.00 O 278 8.00 N 250 7.00 C 920 6.00 H 1430 1.00 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: 2.20 Conformation dependent library (CDL) restraints added in 283.4 milliseconds 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.553A pdb=" N LYS A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.757A pdb=" N ALA A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.553A pdb=" N LYS B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.758A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Proline residue: B 77 - end of helix No H-bonds generated for 'chain 'B' and resid 74 through 79' Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1430 1.03 - 1.22: 3 1.22 - 1.42: 616 1.42 - 1.61: 853 1.61 - 1.80: 8 Bond restraints: 2910 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.95e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.83e+00 bond pdb=" N LEU B 83 " pdb=" CA LEU B 83 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N LEU B 83 " pdb=" H LEU B 83 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.42e+00 ... (remaining 2905 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 49 105.51 - 112.62: 3274 112.62 - 119.74: 854 119.74 - 126.86: 1054 126.86 - 133.97: 23 Bond angle restraints: 5254 Sorted by residual: angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 112.49 103.08 9.41 1.21e+00 6.83e-01 6.04e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 112.49 103.14 9.35 1.21e+00 6.83e-01 5.97e+01 angle pdb=" N LYS B 9 " pdb=" CA LYS B 9 " pdb=" C LYS B 9 " ideal model delta sigma weight residual 112.89 106.94 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" N GLU B 36 " pdb=" CA GLU B 36 " pdb=" C GLU B 36 " ideal model delta sigma weight residual 110.58 117.63 -7.05 1.56e+00 4.11e-01 2.04e+01 angle pdb=" N VAL B 35 " pdb=" CA VAL B 35 " pdb=" C VAL B 35 " ideal model delta sigma weight residual 111.45 115.61 -4.16 9.30e-01 1.16e+00 2.01e+01 ... (remaining 5249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1071 17.93 - 35.87: 63 35.87 - 53.80: 16 53.80 - 71.74: 2 71.74 - 89.67: 6 Dihedral angle restraints: 1158 sinusoidal: 546 harmonic: 612 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 74 " pdb=" C LEU B 74 " pdb=" N SER B 75 " pdb=" CA SER B 75 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A 56 " pdb=" C LEU A 56 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta harmonic sigma weight residual 180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 214 0.153 - 0.306: 4 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.765: 2 Chirality restraints: 220 Sorted by residual: chirality pdb=" CG LEU A 74 " pdb=" CB LEU A 74 " pdb=" CD1 LEU A 74 " pdb=" CD2 LEU A 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ALA A 34 " pdb=" N ALA A 34 " pdb=" C ALA A 34 " pdb=" CB ALA A 34 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 217 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C MET B 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 59 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C MET A 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET A 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 76 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 77 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.045 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 34 2.00 - 2.65: 4114 2.65 - 3.30: 8622 3.30 - 3.95: 10370 3.95 - 4.60: 15836 Nonbonded interactions: 38976 Sorted by model distance: nonbonded pdb=" OG SER A 75 " pdb=" HG SER B 75 " model vdw 1.355 1.850 nonbonded pdb=" O GLY B 30 " pdb=" HG SER B 33 " model vdw 1.488 1.850 nonbonded pdb=" O GLY A 30 " pdb=" HG SER A 33 " model vdw 1.520 1.850 nonbonded pdb=" OD1 ASP B 49 " pdb=" HH TYR B 64 " model vdw 1.659 1.850 nonbonded pdb=" O ILE A 87 " pdb=" HG1 THR A 91 " model vdw 1.713 1.850 ... (remaining 38971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 920 2.51 5 N 250 2.21 5 O 278 1.98 5 H 1430 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 1.230 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: 0.040 Extract box with map and model: 6.750 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 0.068 1480 Z= 0.527 Angle : 1.188 9.406 2006 Z= 0.756 Chirality : 0.089 0.765 220 Planarity : 0.011 0.081 260 Dihedral : 15.190 89.671 546 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 0.00 % 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: -5.77 (0.42), residues: 178 helix: -3.50 (0.29), residues: 134 sheet: None (None), residues: 0 loop : -4.10 (0.72), residues: 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.3588 time to fit residues: 13.4284 Evaluate side-chains 27 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 1480 Z= 0.192 Angle : 0.672 6.597 2006 Z= 0.354 Chirality : 0.036 0.102 220 Planarity : 0.007 0.057 260 Dihedral : 6.131 23.382 196 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.00 % 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: -4.17 (0.52), residues: 178 helix: -2.34 (0.37), residues: 138 sheet: None (None), residues: 0 loop : -3.55 (0.76), residues: 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.4225 time to fit residues: 11.5714 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 1480 Z= 0.144 Angle : 0.577 6.507 2006 Z= 0.297 Chirality : 0.035 0.108 220 Planarity : 0.005 0.051 260 Dihedral : 5.300 20.047 196 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.57), residues: 178 helix: -1.68 (0.40), residues: 140 sheet: None (None), residues: 0 loop : -3.65 (0.88), residues: 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.4278 time to fit residues: 11.7148 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0722 time to fit residues: 0.4014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 1480 Z= 0.160 Angle : 0.584 6.830 2006 Z= 0.306 Chirality : 0.035 0.106 220 Planarity : 0.004 0.034 260 Dihedral : 5.023 18.458 196 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.00 % 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: -2.92 (0.60), residues: 178 helix: -1.40 (0.41), residues: 148 sheet: None (None), residues: 0 loop : -3.77 (1.08), residues: 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.4021 time to fit residues: 10.2656 Evaluate side-chains 24 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 1480 Z= 0.192 Angle : 0.590 7.649 2006 Z= 0.314 Chirality : 0.035 0.105 220 Planarity : 0.004 0.029 260 Dihedral : 4.951 17.626 196 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 1.32 % 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: -2.81 (0.61), residues: 178 helix: -1.35 (0.40), residues: 156 sheet: None (None), residues: 0 loop : -4.24 (1.35), residues: 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.3849 time to fit residues: 10.2286 Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0573 time to fit residues: 0.4702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 1480 Z= 0.146 Angle : 0.538 5.321 2006 Z= 0.284 Chirality : 0.034 0.107 220 Planarity : 0.003 0.030 260 Dihedral : 4.776 16.967 196 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.00 % 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: -2.23 (0.62), residues: 178 helix: -0.96 (0.40), residues: 156 sheet: None (None), residues: 0 loop : -4.10 (1.40), residues: 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.4021 time to fit residues: 9.8063 Evaluate side-chains 22 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 1480 Z= 0.152 Angle : 0.522 3.993 2006 Z= 0.281 Chirality : 0.034 0.103 220 Planarity : 0.003 0.028 260 Dihedral : 4.530 16.043 196 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.66 % 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: -1.83 (0.63), residues: 178 helix: -0.68 (0.41), residues: 156 sheet: None (None), residues: 0 loop : -4.08 (1.46), residues: 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.4040 time to fit residues: 9.9034 Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0490 time to fit residues: 0.3816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 1480 Z= 0.145 Angle : 0.535 4.782 2006 Z= 0.279 Chirality : 0.035 0.108 220 Planarity : 0.003 0.029 260 Dihedral : 4.518 15.481 196 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.66 % 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: -1.52 (0.62), residues: 178 helix: -0.45 (0.41), residues: 156 sheet: None (None), residues: 0 loop : -4.14 (1.35), residues: 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.4053 time to fit residues: 9.4244 Evaluate side-chains 20 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 1480 Z= 0.136 Angle : 0.520 4.924 2006 Z= 0.269 Chirality : 0.034 0.103 220 Planarity : 0.003 0.029 260 Dihedral : 4.313 14.416 196 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.00 % 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: -0.97 (0.64), residues: 178 helix: -0.05 (0.41), residues: 156 sheet: None (None), residues: 0 loop : -4.24 (1.31), residues: 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.4028 time to fit residues: 9.3907 Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 1480 Z= 0.136 Angle : 0.520 4.893 2006 Z= 0.268 Chirality : 0.034 0.102 220 Planarity : 0.003 0.028 260 Dihedral : 4.192 13.892 196 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.00 % 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: -0.67 (0.63), residues: 178 helix: 0.19 (0.41), residues: 156 sheet: None (None), residues: 0 loop : -4.53 (1.08), residues: 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.4163 time to fit residues: 9.7630 Evaluate side-chains 21 residues out of total 152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.077246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.069712 restraints weight = 45447.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.071557 restraints weight = 26608.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.072829 restraints weight = 16909.897| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 1480 Z= 0.140 Angle : 0.523 4.935 2006 Z= 0.270 Chirality : 0.034 0.102 220 Planarity : 0.003 0.028 260 Dihedral : 4.162 14.276 196 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.00 % 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: -0.40 (0.64), residues: 178 helix: 0.39 (0.42), residues: 156 sheet: None (None), residues: 0 loop : -4.59 (1.03), residues: 22 =============================================================================== Job complete usr+sys time: 1769.71 seconds wall clock time: 32 minutes 0.08 seconds (1920.08 seconds total)