Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 09:52:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m64_23688/08_2023/7m64_23688_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1140 2.51 5 N 330 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 1850 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "B" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "F" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "G" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "J" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 185 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Time building chain proxies: 1.24, per 1000 atoms: 0.67 Number of scatterers: 1850 At special positions: 0 Unit cell: (48.53, 66.465, 44.31, 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 380 8.00 N 330 7.00 C 1140 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 259.3 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.94 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: 300 1.29 - 1.36: 323 1.36 - 1.43: 267 1.43 - 1.50: 297 1.50 - 1.56: 693 Bond restraints: 1880 Sorted by residual: bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.32e+00 bond pdb=" C ALA C 13 " pdb=" N ASN C 14 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.25e-02 6.40e+03 4.29e+00 bond pdb=" N ALA F 13 " pdb=" CA ALA F 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 bond pdb=" N ALA H 13 " pdb=" CA ALA H 13 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.27e+00 ... (remaining 1875 not shown) Histogram of bond angle deviations from ideal: 105.94 - 110.97: 691 110.97 - 116.01: 554 116.01 - 121.04: 672 121.04 - 126.08: 633 126.08 - 131.12: 10 Bond angle restraints: 2560 Sorted by residual: angle pdb=" C ALA H 13 " pdb=" CA ALA H 13 " pdb=" CB ALA H 13 " ideal model delta sigma weight residual 110.50 116.35 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta sigma weight residual 110.50 116.34 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA B 13 " pdb=" CA ALA B 13 " pdb=" CB ALA B 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta sigma weight residual 110.50 116.33 -5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C ALA F 13 " pdb=" CA ALA F 13 " pdb=" CB ALA F 13 " ideal model delta sigma weight residual 110.50 116.32 -5.82 1.50e+00 4.44e-01 1.51e+01 ... (remaining 2555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.60: 760 5.60 - 11.20: 140 11.20 - 16.80: 59 16.80 - 22.40: 61 22.40 - 27.99: 20 Dihedral angle restraints: 1040 sinusoidal: 330 harmonic: 710 Sorted by residual: dihedral pdb=" C ALA J 13 " pdb=" N ALA J 13 " pdb=" CA ALA J 13 " pdb=" CB ALA J 13 " ideal model delta harmonic sigma weight residual -122.60 -132.53 9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" C ALA C 13 " pdb=" N ALA C 13 " pdb=" CA ALA C 13 " pdb=" CB ALA C 13 " ideal model delta harmonic sigma weight residual -122.60 -132.51 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" C ALA E 13 " pdb=" N ALA E 13 " pdb=" CA ALA E 13 " pdb=" CB ALA E 13 " ideal model delta harmonic sigma weight residual -122.60 -132.49 9.89 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 224 0.045 - 0.090: 36 0.090 - 0.135: 11 0.135 - 0.179: 9 0.179 - 0.224: 20 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ALA J 13 " pdb=" N ALA J 13 " pdb=" C ALA J 13 " pdb=" CB ALA J 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA C 13 " pdb=" N ALA C 13 " pdb=" C ALA C 13 " pdb=" CB ALA C 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA G 13 " pdb=" N ALA G 13 " pdb=" C ALA G 13 " pdb=" CB ALA G 13 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 297 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 13 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA F 13 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA F 13 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN F 14 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 13 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C ALA C 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA C 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 13 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA H 13 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA H 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN H 14 " -0.008 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 998 2.94 - 3.43: 2268 3.43 - 3.92: 2957 3.92 - 4.41: 3341 4.41 - 4.90: 6391 Nonbonded interactions: 15955 Sorted by model distance: nonbonded pdb=" OG SER I 19 " pdb=" OD1 ASN I 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER A 19 " pdb=" OD1 ASN A 22 " model vdw 2.451 2.440 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.451 2.440 ... (remaining 15950 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.610 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.040 1880 Z= 0.438 Angle : 1.151 5.847 2560 Z= 0.674 Chirality : 0.068 0.224 300 Planarity : 0.004 0.013 340 Dihedral : 10.068 27.994 580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -3.84 (0.40), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0704 time to fit residues: 2.9119 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.014 1880 Z= 0.130 Angle : 0.774 7.370 2560 Z= 0.377 Chirality : 0.045 0.120 300 Planarity : 0.002 0.007 340 Dihedral : 4.380 11.216 250 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.95 % 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: -3.81 (0.39), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.204 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.0666 time to fit residues: 2.6899 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0228 time to fit residues: 0.2969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 30.0000 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 30.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 1880 Z= 0.140 Angle : 0.697 6.102 2560 Z= 0.354 Chirality : 0.044 0.127 300 Planarity : 0.002 0.008 340 Dihedral : 4.252 11.914 250 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.48 % 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: -3.86 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.29), residues: 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.216 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0705 time to fit residues: 2.0434 Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 1880 Z= 0.142 Angle : 0.722 6.849 2560 Z= 0.353 Chirality : 0.044 0.127 300 Planarity : 0.002 0.007 340 Dihedral : 4.184 10.585 250 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.43 % 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: -3.92 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.28), residues: 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.215 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.0965 time to fit residues: 2.4689 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0240 time to fit residues: 0.3170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 1880 Z= 0.174 Angle : 0.720 5.731 2560 Z= 0.366 Chirality : 0.044 0.134 300 Planarity : 0.002 0.008 340 Dihedral : 4.405 11.116 250 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.43 % 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: -3.95 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.28), residues: 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.196 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 20 average time/residue: 0.0496 time to fit residues: 1.4516 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 1880 Z= 0.183 Angle : 0.729 5.736 2560 Z= 0.368 Chirality : 0.043 0.134 300 Planarity : 0.002 0.009 340 Dihedral : 4.447 11.290 250 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.90 % 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: -4.00 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.28), residues: 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.212 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 19 average time/residue: 0.0680 time to fit residues: 1.9096 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0237 time to fit residues: 0.2953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 1880 Z= 0.196 Angle : 0.756 5.843 2560 Z= 0.384 Chirality : 0.044 0.137 300 Planarity : 0.002 0.012 340 Dihedral : 4.619 12.261 250 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.48 % 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: -3.99 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.28), residues: 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.213 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.0664 time to fit residues: 1.9250 Evaluate side-chains 16 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 0.0370 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.6064 ------------------------------------------------------------------------------- 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: 0.7487 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 1880 Z= 0.116 Angle : 0.712 7.379 2560 Z= 0.341 Chirality : 0.043 0.127 300 Planarity : 0.002 0.009 340 Dihedral : 4.333 11.760 250 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -3.97 (0.35), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.27), residues: 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.217 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0657 time to fit residues: 1.5335 Evaluate side-chains 13 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 40.0000 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 overall best weight: 12.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 1880 Z= 0.277 Angle : 0.836 6.918 2560 Z= 0.427 Chirality : 0.045 0.138 300 Planarity : 0.003 0.011 340 Dihedral : 4.879 13.079 250 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.95 % 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: -3.97 (0.37), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.29), residues: 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.230 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 19 average time/residue: 0.0741 time to fit residues: 2.0711 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 1880 Z= 0.152 Angle : 0.749 7.210 2560 Z= 0.362 Chirality : 0.043 0.130 300 Planarity : 0.002 0.010 340 Dihedral : 4.554 13.060 250 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.48 % 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: -3.97 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.27), residues: 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.201 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.0664 time to fit residues: 1.5734 Evaluate side-chains 12 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 40.0000 chunk 18 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.098103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.088492 restraints weight = 6092.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.090494 restraints weight = 2958.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.091981 restraints weight = 1783.087| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.018 1880 Z= 0.161 Angle : 0.770 7.000 2560 Z= 0.376 Chirality : 0.043 0.132 300 Planarity : 0.002 0.013 340 Dihedral : 4.523 13.125 250 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -3.94 (0.36), residues: 230 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.28), residues: 230 =============================================================================== Job complete usr+sys time: 654.42 seconds wall clock time: 13 minutes 44.36 seconds (824.36 seconds total)