Starting phenix.real_space_refine (version: dev) on Mon Dec 12 00:29:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsl_12570/12_2022/7nsl_12570.pdb" } resolution = 3.1 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= 1.000 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 "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G ASP 86": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8323 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "C" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "B" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "A" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "G" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 4.36, per 1000 atoms: 0.52 Number of scatterers: 8323 At special positions: 0 Unit cell: (64.48, 98.8, 58.24, 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 14 16.00 O 910 8.00 N 679 7.00 C 2667 6.00 H 4053 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.02 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: 6.31 Conformation dependent library (CDL) restraints added in 649.2 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 44 current: chain 'B' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 44 current: chain 'C' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 44 current: chain 'D' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 44 current: chain 'E' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 44 current: chain 'F' and resid 43 through 44 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 74 Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 88 through 89 current: chain 'B' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 88 through 89 current: chain 'C' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 88 through 89 current: chain 'D' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 89 current: chain 'E' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 88 through 89 current: chain 'F' and resid 88 through 89 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 107 180 hydrogen bonds defined for protein. 540 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: 3.20 Time building geometry restraints manager: 6.60 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: 4053 1.03 - 1.23: 125 1.23 - 1.42: 1730 1.42 - 1.61: 2478 1.61 - 1.81: 14 Bond restraints: 8400 Sorted by residual: bond pdb=" CA ALA G 44 " pdb=" CB ALA G 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA A 44 " pdb=" CB ALA A 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA B 44 " pdb=" CB ALA B 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.48e+01 bond pdb=" CA ALA E 44 " pdb=" CB ALA E 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.47e+01 bond pdb=" CA ALA F 44 " pdb=" CB ALA F 44 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.17e-02 7.31e+03 5.46e+01 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.59: 745 107.59 - 114.23: 9558 114.23 - 120.88: 2545 120.88 - 127.53: 2159 127.53 - 134.18: 50 Bond angle restraints: 15057 Sorted by residual: angle pdb=" CA GLY G 90 " pdb=" C GLY G 90 " pdb=" O GLY G 90 " ideal model delta sigma weight residual 120.91 114.30 6.61 6.90e-01 2.10e+00 9.18e+01 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 120.91 114.34 6.57 6.90e-01 2.10e+00 9.06e+01 angle pdb=" CA GLY E 90 " pdb=" C GLY E 90 " pdb=" O GLY E 90 " ideal model delta sigma weight residual 120.91 114.35 6.56 6.90e-01 2.10e+00 9.03e+01 angle pdb=" CA GLY B 90 " pdb=" C GLY B 90 " pdb=" O GLY B 90 " ideal model delta sigma weight residual 120.91 114.36 6.55 6.90e-01 2.10e+00 9.01e+01 angle pdb=" CA GLY F 90 " pdb=" C GLY F 90 " pdb=" O GLY F 90 " ideal model delta sigma weight residual 120.91 114.37 6.54 6.90e-01 2.10e+00 8.97e+01 ... (remaining 15052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 2870 16.17 - 32.34: 343 32.34 - 48.51: 70 48.51 - 64.68: 56 64.68 - 80.86: 7 Dihedral angle restraints: 3346 sinusoidal: 1449 harmonic: 1897 Sorted by residual: dihedral pdb=" N LEU F 97 " pdb=" CA LEU F 97 " pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU C 97 " pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" CB LEU B 97 " pdb=" CG LEU B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 3343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 390 0.056 - 0.111: 188 0.111 - 0.167: 67 0.167 - 0.222: 34 0.222 - 0.278: 14 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA LEU A 47 " pdb=" N LEU A 47 " pdb=" C LEU A 47 " pdb=" CB LEU A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU B 47 " pdb=" N LEU B 47 " pdb=" C LEU B 47 " pdb=" CB LEU B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LEU F 47 " pdb=" N LEU F 47 " pdb=" C LEU F 47 " pdb=" CB LEU F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 690 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN E 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN E 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN E 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN E 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN G 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN G 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN G 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN G 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN D 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN D 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN D 16 " -0.546 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 427 2.18 - 2.78: 16305 2.78 - 3.39: 22336 3.39 - 3.99: 32827 3.99 - 4.60: 47613 Nonbonded interactions: 119508 Sorted by model distance: nonbonded pdb=" HG1 THR A 81 " pdb=" OD1 ASP A 83 " model vdw 1.572 1.850 nonbonded pdb=" HG1 THR E 81 " pdb=" OD1 ASP E 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR F 81 " pdb=" OD1 ASP F 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR G 81 " pdb=" OD1 ASP G 83 " model vdw 1.573 1.850 nonbonded pdb=" HG1 THR D 81 " pdb=" OD1 ASP D 83 " model vdw 1.573 1.850 ... (remaining 119503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 14 5.16 5 C 2667 2.51 5 N 679 2.21 5 O 910 1.98 5 H 4053 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.110 Extract box with map and model: 4.040 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 30.490 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.012 0.087 4347 Z= 0.814 Angle : 1.845 8.934 5929 Z= 1.282 Chirality : 0.084 0.278 693 Planarity : 0.014 0.039 749 Dihedral : 14.483 80.856 1442 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -5.51 (0.17), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.13), residues: 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2403 time to fit residues: 64.2424 Evaluate side-chains 152 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 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: 0.7840 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4347 Z= 0.196 Angle : 0.634 4.000 5929 Z= 0.340 Chirality : 0.045 0.157 693 Planarity : 0.003 0.022 749 Dihedral : 6.426 16.576 616 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 4.76 % 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: -4.94 (0.19), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.15), residues: 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.2417 time to fit residues: 53.6698 Evaluate side-chains 170 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1014 time to fit residues: 3.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 4347 Z= 0.320 Angle : 0.693 5.691 5929 Z= 0.362 Chirality : 0.046 0.138 693 Planarity : 0.003 0.022 749 Dihedral : 6.087 14.307 616 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.23), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.18), residues: 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.2651 time to fit residues: 52.9911 Evaluate side-chains 146 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1188 time to fit residues: 2.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8015 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4347 Z= 0.240 Angle : 0.613 4.708 5929 Z= 0.320 Chirality : 0.044 0.143 693 Planarity : 0.003 0.026 749 Dihedral : 6.027 16.819 616 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 3.46 % 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: -4.21 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.18), residues: 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.698 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.2624 time to fit residues: 51.8775 Evaluate side-chains 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 0.601 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1153 time to fit residues: 3.0743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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: 0.8030 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 4347 Z= 0.235 Angle : 0.595 4.329 5929 Z= 0.312 Chirality : 0.044 0.134 693 Planarity : 0.003 0.025 749 Dihedral : 5.907 15.524 616 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.95 % 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: -4.18 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.680 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 0.2543 time to fit residues: 48.9280 Evaluate side-chains 140 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1091 time to fit residues: 1.5910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4347 Z= 0.227 Angle : 0.595 5.511 5929 Z= 0.310 Chirality : 0.044 0.136 693 Planarity : 0.003 0.025 749 Dihedral : 5.869 16.463 616 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 0.661 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.2561 time to fit residues: 47.1829 Evaluate side-chains 143 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1081 time to fit residues: 2.4616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4347 Z= 0.186 Angle : 0.568 4.138 5929 Z= 0.296 Chirality : 0.043 0.134 693 Planarity : 0.003 0.027 749 Dihedral : 5.777 15.198 616 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 0.65 % 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: -4.16 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 134 average time/residue: 0.2663 time to fit residues: 47.1419 Evaluate side-chains 132 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4347 Z= 0.286 Angle : 0.604 4.252 5929 Z= 0.317 Chirality : 0.044 0.135 693 Planarity : 0.003 0.026 749 Dihedral : 5.867 15.558 616 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 1.73 % 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: -4.18 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.718 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.2664 time to fit residues: 45.8636 Evaluate side-chains 133 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1001 time to fit residues: 1.8565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4347 Z= 0.213 Angle : 0.578 4.235 5929 Z= 0.302 Chirality : 0.044 0.137 693 Planarity : 0.003 0.027 749 Dihedral : 5.789 15.557 616 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 0.43 % 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: -4.14 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.19), residues: 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.682 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2602 time to fit residues: 44.3748 Evaluate side-chains 127 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0983 time to fit residues: 0.9622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4347 Z= 0.189 Angle : 0.580 4.110 5929 Z= 0.302 Chirality : 0.044 0.142 693 Planarity : 0.003 0.026 749 Dihedral : 5.740 15.814 616 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.19), residues: 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.677 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.2654 time to fit residues: 46.7699 Evaluate side-chains 130 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1027 time to fit residues: 1.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.109171 restraints weight = 18283.102| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.76 r_work: 0.3706 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 4347 Z= 0.301 Angle : 0.602 3.886 5929 Z= 0.316 Chirality : 0.044 0.137 693 Planarity : 0.003 0.026 749 Dihedral : 5.787 16.689 616 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 567 =============================================================================== Job complete usr+sys time: 3138.08 seconds wall clock time: 55 minutes 51.94 seconds (3351.94 seconds total)