Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:47:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4d_31708/11_2022/7v4d_31708.pdb" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2376 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 396 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 1.71, per 1000 atoms: 0.72 Number of scatterers: 2376 At special positions: 0 Unit cell: (98.58, 87.98, 31.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 480 8.00 N 408 7.00 C 1488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 362.3 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.367A pdb=" N LYS F 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.128A pdb=" N GLN F 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.361A pdb=" N LYS E 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'E' and resid 62 through 63 removed outlier: 6.129A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'E' and resid 81 through 82 20 hydrogen bonds defined for protein. 60 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: 0.50 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 414 1.29 - 1.35: 373 1.35 - 1.42: 102 1.42 - 1.48: 401 1.48 - 1.55: 1098 Bond restraints: 2388 Sorted by residual: bond pdb=" CA LEU D 38 " pdb=" C LEU D 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.42e-01 bond pdb=" CA LEU F 38 " pdb=" C LEU F 38 " ideal model delta sigma weight residual 1.523 1.533 -0.011 1.10e-02 8.26e+03 9.17e-01 bond pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.07e-01 bond pdb=" CA LEU E 38 " pdb=" C LEU E 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 9.04e-01 bond pdb=" CA LEU C 38 " pdb=" C LEU C 38 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.62e-01 ... (remaining 2383 not shown) Histogram of bond angle deviations from ideal: 106.13 - 111.14: 1035 111.14 - 116.14: 716 116.14 - 121.15: 679 121.15 - 126.16: 804 126.16 - 131.16: 6 Bond angle restraints: 3240 Sorted by residual: angle pdb=" CA ASN B 65 " pdb=" CB ASN B 65 " pdb=" CG ASN B 65 " ideal model delta sigma weight residual 112.60 114.52 -1.92 1.00e+00 1.00e+00 3.70e+00 angle pdb=" CA ASN A 65 " pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN E 65 " pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.58e+00 angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.54e+00 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 114.48 -1.88 1.00e+00 1.00e+00 3.52e+00 ... (remaining 3235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.21: 1206 12.21 - 24.43: 132 24.43 - 36.64: 18 36.64 - 48.85: 12 48.85 - 61.07: 6 Dihedral angle restraints: 1374 sinusoidal: 438 harmonic: 936 Sorted by residual: dihedral pdb=" CA VAL A 48 " pdb=" C VAL A 48 " pdb=" N VAL A 49 " pdb=" CA VAL A 49 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL B 48 " pdb=" C VAL B 48 " pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 1371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 214 0.025 - 0.049: 108 0.049 - 0.074: 52 0.074 - 0.099: 34 0.099 - 0.124: 24 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL D 70 " pdb=" N VAL D 70 " pdb=" C VAL D 70 " pdb=" CB VAL D 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 429 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 87 " 0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C SER C 87 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 88 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.29e+00 pdb=" C SER E 87 " 0.020 2.00e-02 2.50e+03 pdb=" O SER E 87 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE E 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 87 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C SER F 87 " -0.019 2.00e-02 2.50e+03 pdb=" O SER F 87 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE F 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 331 2.77 - 3.30: 2209 3.30 - 3.83: 3524 3.83 - 4.37: 3821 4.37 - 4.90: 7885 Nonbonded interactions: 17770 Sorted by model distance: nonbonded pdb=" OE1 GLU A 61 " pdb=" OG1 THR A 72 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU E 61 " pdb=" OG1 THR E 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU C 61 " pdb=" OG1 THR C 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU B 61 " pdb=" OG1 THR B 72 " model vdw 2.235 2.440 nonbonded pdb=" OE1 GLU F 61 " pdb=" OG1 THR F 72 " model vdw 2.235 2.440 ... (remaining 17765 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' } 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: 3 Type Number sf(0) Gaussians C 1488 2.51 5 N 408 2.21 5 O 480 1.98 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.720 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 11.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2388 Z= 0.196 Angle : 0.544 3.405 3240 Z= 0.315 Chirality : 0.045 0.124 432 Planarity : 0.002 0.011 402 Dihedral : 11.888 61.066 786 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -5.68 (0.26), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.20), residues: 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0800 time to fit residues: 4.2648 Evaluate side-chains 35 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 2388 Z= 0.309 Angle : 0.618 4.989 3240 Z= 0.340 Chirality : 0.046 0.132 432 Planarity : 0.003 0.012 402 Dihedral : 5.200 17.145 348 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer Outliers : 7.50 % 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: -5.30 (0.29), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.22), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 35 time to evaluate : 0.276 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 50 average time/residue: 0.0830 time to fit residues: 5.4677 Evaluate side-chains 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0251 time to fit residues: 0.9863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2388 Z= 0.168 Angle : 0.545 4.431 3240 Z= 0.306 Chirality : 0.046 0.149 432 Planarity : 0.002 0.013 402 Dihedral : 4.763 17.638 348 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 5.00 % 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: -4.77 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.25), residues: 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.260 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0718 time to fit residues: 4.8942 Evaluate side-chains 43 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0342 time to fit residues: 0.6740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 2388 Z= 0.337 Angle : 0.645 5.885 3240 Z= 0.354 Chirality : 0.047 0.203 432 Planarity : 0.003 0.014 402 Dihedral : 5.163 18.031 348 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.25), residues: 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.292 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.0726 time to fit residues: 4.3848 Evaluate side-chains 42 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0254 time to fit residues: 0.7616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 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: 0.7972 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2388 Z= 0.202 Angle : 0.600 6.984 3240 Z= 0.331 Chirality : 0.047 0.172 432 Planarity : 0.002 0.015 402 Dihedral : 4.814 17.365 348 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 5.00 % 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: -4.47 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.26), residues: 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.224 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 44 average time/residue: 0.0630 time to fit residues: 3.9175 Evaluate side-chains 36 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0229 time to fit residues: 0.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 2388 Z= 0.343 Angle : 0.672 6.023 3240 Z= 0.367 Chirality : 0.048 0.160 432 Planarity : 0.003 0.016 402 Dihedral : 5.225 17.793 348 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.26), residues: 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.280 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 37 average time/residue: 0.0729 time to fit residues: 3.8082 Evaluate side-chains 40 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0304 time to fit residues: 0.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 2388 Z= 0.156 Angle : 0.586 5.572 3240 Z= 0.322 Chirality : 0.048 0.166 432 Planarity : 0.003 0.021 402 Dihedral : 4.553 17.028 348 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.67 % 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 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.27), residues: 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.246 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0716 time to fit residues: 3.6661 Evaluate side-chains 31 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0240 time to fit residues: 0.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 2388 Z= 0.259 Angle : 0.621 7.723 3240 Z= 0.334 Chirality : 0.047 0.159 432 Planarity : 0.002 0.019 402 Dihedral : 4.802 17.415 348 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer Outliers : 2.08 % 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: -4.06 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.27), residues: 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.282 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.0854 time to fit residues: 3.9427 Evaluate side-chains 33 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0264 time to fit residues: 0.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 2388 Z= 0.248 Angle : 0.627 7.722 3240 Z= 0.338 Chirality : 0.047 0.158 432 Planarity : 0.003 0.021 402 Dihedral : 4.845 17.138 348 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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: -4.02 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.27), residues: 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.259 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0832 time to fit residues: 3.5412 Evaluate side-chains 27 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2388 Z= 0.180 Angle : 0.579 7.555 3240 Z= 0.310 Chirality : 0.047 0.160 432 Planarity : 0.003 0.019 402 Dihedral : 4.496 17.145 348 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 0.42 % 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: -3.77 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.29), residues: 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.265 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.0791 time to fit residues: 3.2691 Evaluate side-chains 28 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0261 time to fit residues: 0.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.173712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.146075 restraints weight = 2555.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.149560 restraints weight = 1258.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.151788 restraints weight = 849.378| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2388 Z= 0.177 Angle : 0.568 8.238 3240 Z= 0.301 Chirality : 0.047 0.159 432 Planarity : 0.003 0.020 402 Dihedral : 4.387 16.734 348 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % 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: -3.57 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.30), residues: 336 =============================================================================== Job complete usr+sys time: 896.29 seconds wall clock time: 17 minutes 22.40 seconds (1042.40 seconds total)