Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:28:54 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x1g_6701/01_2021/5x1g_6701.pdb" } resolution = 4.5 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= -0.030 sd= 0.888 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 155 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 0.41, per 1000 atoms: 2.65 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 155 At special positions: 0 Unit cell: (32.65, 47.016, 56.158, 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 31 8.00 N 31 7.00 C 93 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 Amimo 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: 0.07 Conformation dependent library (CDL) restraints added in 35.9 milliseconds 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 62 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'C' and resid 524 through 541 removed outlier: 3.904A pdb=" N LYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 14 hydrogen bonds defined for protein. 42 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: 0.04 Time building geometry restraints manager: 0.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 31 1.29 - 1.35: 30 1.35 - 1.41: 0 1.41 - 1.48: 31 1.48 - 1.54: 62 Bond restraints: 154 Sorted by residual: bond pdb=" N LYS C 546 " pdb=" CA LYS C 546 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" CA PHE C 545 " pdb=" C PHE C 545 " ideal model delta sigma weight residual 1.522 1.506 0.017 1.37e-02 5.33e+03 1.46e+00 bond pdb=" C PHE C 545 " pdb=" N LYS C 546 " ideal model delta sigma weight residual 1.329 1.312 0.017 1.40e-02 5.10e+03 1.41e+00 bond pdb=" CA TRP C 530 " pdb=" C TRP C 530 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.35e-02 5.49e+03 1.35e+00 bond pdb=" CA LYS C 516 " pdb=" C LYS C 516 " ideal model delta sigma weight residual 1.525 1.501 0.024 2.10e-02 2.27e+03 1.34e+00 ... (remaining 149 not shown) Histogram of bond angle deviations from ideal: 105.66 - 109.91: 24 109.91 - 114.15: 69 114.15 - 118.40: 30 118.40 - 122.64: 75 122.64 - 126.89: 16 Bond angle restraints: 214 Sorted by residual: angle pdb=" N GLU C 523 " pdb=" CA GLU C 523 " pdb=" C GLU C 523 " ideal model delta sigma weight residual 108.32 113.41 -5.09 1.64e+00 3.72e-01 9.65e+00 angle pdb=" C LYS C 521 " pdb=" N GLU C 522 " pdb=" CA GLU C 522 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.84e+00 angle pdb=" C GLU C 523 " pdb=" N GLU C 524 " pdb=" CA GLU C 524 " ideal model delta sigma weight residual 122.36 125.86 -3.50 1.42e+00 4.96e-01 6.09e+00 angle pdb=" N SER C 544 " pdb=" CA SER C 544 " pdb=" C SER C 544 " ideal model delta sigma weight residual 113.97 110.92 3.05 1.28e+00 6.10e-01 5.70e+00 angle pdb=" N PHE C 545 " pdb=" CA PHE C 545 " pdb=" C PHE C 545 " ideal model delta sigma weight residual 113.18 110.46 2.72 1.21e+00 6.83e-01 5.05e+00 ... (remaining 209 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 4.71: 73 4.71 - 9.40: 6 9.40 - 14.09: 9 14.09 - 18.78: 3 18.78 - 23.47: 1 Dihedral angle restraints: 92 sinusoidal: 0 harmonic: 92 Sorted by residual: dihedral pdb=" CA LYS C 521 " pdb=" C LYS C 521 " pdb=" N GLU C 522 " pdb=" CA GLU C 522 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA THR C 538 " pdb=" C THR C 538 " pdb=" N LEU C 539 " pdb=" CA LEU C 539 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLN C 540 " pdb=" C GLN C 540 " pdb=" N ARG C 541 " pdb=" CA ARG C 541 " ideal model delta harmonic sigma weight residual -180.00 -164.45 -15.55 0 5.00e+00 4.00e-02 9.67e+00 ... (remaining 89 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.038: 21 0.038 - 0.072: 8 0.072 - 0.106: 1 0.106 - 0.140: 0 0.140 - 0.174: 1 Chirality restraints: 31 Sorted by residual: chirality pdb=" CA LYS C 516 " pdb=" N LYS C 516 " pdb=" C LYS C 516 " pdb=" CB LYS C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 520 " pdb=" N ILE C 520 " pdb=" C ILE C 520 " pdb=" CB ILE C 520 " both_signs ideal model delta sigma weight residual False 2.43 2.51 -0.08 2.00e-01 2.50e+01 1.49e-01 chirality pdb=" CA GLU C 524 " pdb=" N GLU C 524 " pdb=" C GLU C 524 " pdb=" CB GLU C 524 " both_signs ideal model delta sigma weight residual False 2.51 2.44 0.07 2.00e-01 2.50e+01 1.17e-01 ... (remaining 28 not shown) Planarity restraints: 30 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 542 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C LEU C 542 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU C 542 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG C 543 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 522 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLU C 522 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU C 522 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU C 523 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 537 " -0.004 2.00e-02 2.50e+03 8.12e-03 6.60e-01 pdb=" C LYS C 537 " 0.014 2.00e-02 2.50e+03 pdb=" O LYS C 537 " -0.005 2.00e-02 2.50e+03 pdb=" N THR C 538 " -0.005 2.00e-02 2.50e+03 ... (remaining 27 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 102 3.04 - 3.50: 182 3.50 - 3.97: 179 3.97 - 4.43: 262 4.43 - 4.90: 278 Nonbonded interactions: 1003 Sorted by model distance: nonbonded pdb=" N LYS C 546 " pdb=" O LYS C 546 " model vdw 2.572 2.496 nonbonded pdb=" N ASP C 518 " pdb=" O ASP C 518 " model vdw 2.577 2.496 nonbonded pdb=" N LYS C 521 " pdb=" O LYS C 521 " model vdw 2.618 2.496 nonbonded pdb=" N PHE C 545 " pdb=" N LYS C 546 " model vdw 2.625 2.560 nonbonded pdb=" N ILE C 520 " pdb=" O ILE C 520 " model vdw 2.636 2.496 ... (remaining 998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 155 True False 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 93 2.51 5 N 31 2.21 5 O 31 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 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: 9.100 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.170 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.110 Process input model: 10.980 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.240 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.031 154 Angle : 1.425 5.348 214 Chirality : 0.048 0.174 31 Planarity : 0.006 0.014 30 Dihedral : 10.047 23.473 30 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (1.40), residues: 29 helix: -3.91 (0.83), residues: 12 sheet: None (None), residues: 0 loop : -0.03 (1.51), residues: 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0343 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 90.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.0252 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.004 154 Angle : 0.378 1.682 214 Chirality : 0.032 0.105 31 Planarity : 0.002 0.005 30 Dihedral : 4.704 10.882 30 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (1.33), residues: 29 helix: -0.97 (1.01), residues: 22 sheet: None (None), residues: 0 loop : -4.17 (1.33), residues: 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0335 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 90.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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: 0.0244 moved from start: 0.8325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.002 154 Angle : 0.327 1.446 214 Chirality : 0.032 0.097 31 Planarity : 0.001 0.003 30 Dihedral : 4.152 8.262 30 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (1.57), residues: 29 helix: 1.26 (1.14), residues: 22 sheet: None (None), residues: 0 loop : -4.52 (1.26), residues: 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0358 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 50.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- 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: 0.1059 moved from start: 1.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.005 154 Angle : 0.419 1.952 214 Chirality : 0.032 0.088 31 Planarity : 0.003 0.008 30 Dihedral : 5.765 13.582 30 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (1.66), residues: 29 helix: 1.18 (1.22), residues: 22 sheet: None (None), residues: 0 loop : -4.55 (1.19), residues: 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0345 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 70.0000 chunk 1 optimal weight: 50.0000 chunk 2 optimal weight: 40.0000 overall best weight: 40.0000 ------------------------------------------------------------------------------- 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: 0.1283 moved from start: 2.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.004 154 Angle : 0.416 1.653 214 Chirality : 0.035 0.103 31 Planarity : 0.003 0.009 30 Dihedral : 5.414 14.473 30 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 1.84 (1.54), residues: 29 helix: 3.03 (1.21), residues: 18 sheet: None (None), residues: 0 loop : -2.12 (1.40), residues: 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0345 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 100.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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: 0.1339 moved from start: 2.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.003 154 Angle : 0.289 1.201 214 Chirality : 0.031 0.092 31 Planarity : 0.001 0.004 30 Dihedral : 3.906 8.792 30 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (1.70), residues: 29 helix: 2.95 (1.19), residues: 22 sheet: None (None), residues: 0 loop : -3.98 (1.29), residues: 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0346 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 90.0000 chunk 1 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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: 0.1319 moved from start: 2.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.003 154 Angle : 0.306 1.394 214 Chirality : 0.032 0.094 31 Planarity : 0.001 0.004 30 Dihedral : 4.304 9.714 30 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (1.67), residues: 29 helix: 3.38 (1.13), residues: 22 sheet: None (None), residues: 0 loop : -3.98 (1.39), residues: 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0342 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 100.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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: 0.1365 moved from start: 2.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.002 154 Angle : 0.263 1.235 214 Chirality : 0.031 0.088 31 Planarity : 0.001 0.003 30 Dihedral : 3.378 6.909 30 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 3.55 (1.70), residues: 29 helix: 4.02 (1.12), residues: 22 sheet: None (None), residues: 0 loop : -3.79 (1.49), residues: 7 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0350 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 90.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 50.0000 overall best weight: 40.0000 ------------------------------------------------------------------------------- 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: 0.1270 moved from start: 2.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.002 154 Angle : 0.279 1.264 214 Chirality : 0.031 0.089 31 Planarity : 0.001 0.004 30 Dihedral : 3.864 7.883 30 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 3.37 (1.69), residues: 29 helix: 3.85 (1.12), residues: 22 sheet: None (None), residues: 0 loop : -3.70 (1.53), residues: 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0345 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 90.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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: 0.1366 moved from start: 2.8210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.002 154 Angle : 0.256 1.244 214 Chirality : 0.031 0.090 31 Planarity : 0.001 0.002 30 Dihedral : 3.106 5.895 30 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.25 (1.63), residues: 29 helix: 4.99 (1.02), residues: 20 sheet: None (None), residues: 0 loop : -2.85 (1.52), residues: 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 58 Ramachandran restraints generated. 29 Oldfield and 0 Emsley and 29 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0366 Evaluate side-chains 0 residues out of total 31 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 3 random chunks: chunk 0 optimal weight: 100.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.060969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.052429 restraints weight = 4378.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.052429 restraints weight = 5898.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.052429 restraints weight = 5898.330| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.001 0.002 154 ANGLE : 0.247 1.269 214 CHIRALITY : 0.031 0.084 31 PLANARITY : 0.001 0.003 30 DIHEDRAL : 3.040 6.336 30 MIN NONBONDED DISTANCE : 2.649 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % 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: 4.51 (1.66), RESIDUES: 29 HELIX: 5.09 (1.05), RESIDUES: 20 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -2.48 (1.67), RESIDUES: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1252 moved from start: 2.9019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.001 0.002 154 Angle : 0.247 1.269 214 Chirality : 0.031 0.084 31 Planarity : 0.001 0.003 30 Dihedral : 3.040 6.336 30 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.51 (1.66), residues: 29 helix: 5.09 (1.05), residues: 20 sheet: None (None), residues: 0 loop : -2.48 (1.67), residues: 9 =============================================================================== Job complete usr+sys time: 493.65 seconds wall clock time: 9 minutes 33.30 seconds (573.30 seconds total)