Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:04:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zqe_14872/12_2022/7zqe_14872.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 1423 Number of models: 1 Model: "" Number of chains: 1 Chain: "M" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1423 Unusual residues: {' CU': 1} Inner-chain residues flagged as termini: ['pdbres="GLN M 98 "'] Classifications: {'peptide': 98, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 92, None: 1} Not linked: pdbres="GLN M 98 " pdbres=" CU M 101 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1197 SG CYS M 83 22.202 21.040 12.108 1.00 69.77 S Time building chain proxies: 1.30, per 1000 atoms: 0.91 Number of scatterers: 1423 At special positions: 0 Unit cell: (47.04, 39.48, 45.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 1 28.99 S 2 16.00 O 149 8.00 N 118 7.00 C 459 6.00 H 694 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 161.4 milliseconds 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 174 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 2 sheets defined 7.1% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'M' and resid 84 through 90 removed outlier: 5.271A pdb=" N GLY M 88 " --> pdb=" O PRO M 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.619A pdb=" N TYR M 82 " --> pdb=" O VAL M 41 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 57 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: 0.46 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 694 1.03 - 1.23: 0 1.23 - 1.42: 315 1.42 - 1.61: 425 1.61 - 1.81: 3 Bond restraints: 1437 Sorted by residual: bond pdb=" N ASP M 1 " pdb=" CA ASP M 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N ASP M 1 " pdb=" H ASP M 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" CB PRO M 37 " pdb=" CG PRO M 37 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 3.96e-01 bond pdb=" CG PRO M 48 " pdb=" CD PRO M 48 " ideal model delta sigma weight residual 1.503 1.524 -0.021 3.40e-02 8.65e+02 3.93e-01 bond pdb=" CB PRO M 17 " pdb=" CG PRO M 17 " ideal model delta sigma weight residual 1.506 1.485 0.021 3.90e-02 6.57e+02 2.77e-01 ... (remaining 1432 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.35: 22 106.35 - 112.53: 1640 112.53 - 118.71: 307 118.71 - 124.88: 596 124.88 - 131.06: 29 Bond angle restraints: 2594 Sorted by residual: angle pdb=" CA ASP M 1 " pdb=" N ASP M 1 " pdb=" H ASP M 1 " ideal model delta sigma weight residual 114.00 109.47 4.53 3.00e+00 1.11e-01 2.28e+00 angle pdb=" N PRO M 37 " pdb=" CA PRO M 37 " pdb=" C PRO M 37 " ideal model delta sigma weight residual 112.10 116.01 -3.91 2.60e+00 1.48e-01 2.26e+00 angle pdb=" O PRO M 37 " pdb=" C PRO M 37 " pdb=" N HIS M 38 " ideal model delta sigma weight residual 121.10 123.61 -2.51 1.90e+00 2.77e-01 1.74e+00 angle pdb=" O PRO M 17 " pdb=" C PRO M 17 " pdb=" N LYS M 18 " ideal model delta sigma weight residual 121.10 123.20 -2.10 1.90e+00 2.77e-01 1.22e+00 angle pdb=" N PRO M 48 " pdb=" CD PRO M 48 " pdb=" HD2 PRO M 48 " ideal model delta sigma weight residual 109.00 112.17 -3.17 3.00e+00 1.11e-01 1.11e+00 ... (remaining 2589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.20: 505 9.20 - 18.41: 57 18.41 - 27.61: 5 27.61 - 36.81: 2 36.81 - 46.02: 1 Dihedral angle restraints: 570 sinusoidal: 248 harmonic: 322 Sorted by residual: dihedral pdb=" CA PHE M 36 " pdb=" C PHE M 36 " pdb=" N PRO M 37 " pdb=" CA PRO M 37 " ideal model delta harmonic sigma weight residual 0.00 14.36 -14.36 0 5.00e+00 4.00e-02 8.25e+00 dihedral pdb=" N ARG M 58 " pdb=" CA ARG M 58 " pdb=" CB ARG M 58 " pdb=" CG ARG M 58 " ideal model delta sinusoidal sigma weight residual -60.00 -95.29 35.29 3 1.50e+01 4.44e-03 6.04e+00 dihedral pdb=" CA GLY M 77 " pdb=" C GLY M 77 " pdb=" N GLU M 78 " pdb=" CA GLU M 78 " ideal model delta harmonic sigma weight residual 180.00 168.27 11.73 0 5.00e+00 4.00e-02 5.50e+00 ... (remaining 567 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.032: 72 0.032 - 0.063: 23 0.063 - 0.094: 5 0.094 - 0.125: 12 0.125 - 0.156: 1 Chirality restraints: 113 Sorted by residual: chirality pdb=" CA ILE M 47 " pdb=" N ILE M 47 " pdb=" C ILE M 47 " pdb=" CB ILE M 47 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE M 96 " pdb=" N ILE M 96 " pdb=" C ILE M 96 " pdb=" CB ILE M 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE M 40 " pdb=" N ILE M 40 " pdb=" C ILE M 40 " pdb=" CB ILE M 40 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 110 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 47 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO M 48 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO M 48 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 48 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 77 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY M 77 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY M 77 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU M 78 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 30 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C PHE M 30 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE M 30 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL M 31 " 0.008 2.00e-02 2.50e+03 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 148 2.25 - 2.84: 3268 2.84 - 3.42: 3580 3.42 - 4.01: 5221 4.01 - 4.60: 7594 Nonbonded interactions: 19811 Sorted by model distance: nonbonded pdb=" O ALA M 75 " pdb=" HH TYR M 79 " model vdw 1.662 1.850 nonbonded pdb=" O ALA M 53 " pdb=" HG SER M 57 " model vdw 1.667 1.850 nonbonded pdb=" H SER M 24 " pdb=" O GLN M 98 " model vdw 1.682 1.850 nonbonded pdb=" O ILE M 40 " pdb=" H ARG M 58 " model vdw 1.736 1.850 nonbonded pdb=" O ALA M 34 " pdb=" HE2 HIS M 38 " model vdw 1.775 1.850 ... (remaining 19806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 1 5.60 5 S 2 5.16 5 C 459 2.51 5 N 118 2.21 5 O 149 1.98 5 H 694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.110 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: 0.030 Extract box with map and model: 64.400 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.030 Process input model: 18.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 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 : 0.002 0.032 743 Z= 0.162 Angle : 0.423 4.143 1012 Z= 0.222 Chirality : 0.048 0.156 113 Planarity : 0.006 0.054 136 Dihedral : 7.036 36.617 261 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: -0.73 (0.85), residues: 96 helix: None (None), residues: 0 sheet: -0.70 (0.88), residues: 35 loop : -0.26 (0.80), residues: 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.119 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 1.6886 time to fit residues: 18.8962 Evaluate side-chains 4 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9233 ------------------------------------------------------------------------------- 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: 0.5190 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 743 Z= 0.189 Angle : 0.501 4.195 1012 Z= 0.261 Chirality : 0.046 0.155 113 Planarity : 0.006 0.046 136 Dihedral : 3.953 14.362 104 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: -0.18 (0.85), residues: 96 helix: None (None), residues: 0 sheet: -0.22 (0.90), residues: 32 loop : 0.02 (0.79), residues: 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4 time to evaluate : 0.121 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.5927 time to fit residues: 3.2121 Evaluate side-chains 4 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 743 Z= 0.171 Angle : 0.461 4.127 1012 Z= 0.239 Chirality : 0.046 0.147 113 Planarity : 0.005 0.043 136 Dihedral : 3.762 13.980 104 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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 (0.87), residues: 96 helix: None (None), residues: 0 sheet: 0.06 (0.85), residues: 34 loop : 0.14 (0.85), residues: 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.136 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.7069 time to fit residues: 3.0668 Evaluate side-chains 4 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.169 Angle : 0.454 4.096 1012 Z= 0.236 Chirality : 0.045 0.146 113 Planarity : 0.005 0.041 136 Dihedral : 3.676 13.807 104 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.08 (0.87), residues: 96 helix: None (None), residues: 0 sheet: -0.10 (0.87), residues: 36 loop : 0.28 (0.84), residues: 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.7382 time to fit residues: 3.1865 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.168 Angle : 0.454 4.159 1012 Z= 0.234 Chirality : 0.045 0.143 113 Planarity : 0.005 0.041 136 Dihedral : 3.798 14.618 104 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.13 (0.86), residues: 96 helix: None (None), residues: 0 sheet: 0.02 (0.88), residues: 36 loop : 0.25 (0.82), residues: 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.142 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.8937 time to fit residues: 2.9100 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.156 Angle : 0.437 4.132 1012 Z= 0.227 Chirality : 0.045 0.144 113 Planarity : 0.005 0.041 136 Dihedral : 3.670 12.971 104 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.24 (0.87), residues: 96 helix: None (None), residues: 0 sheet: 0.13 (0.89), residues: 36 loop : 0.29 (0.82), residues: 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.0082 time to fit residues: 2.2317 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.148 Angle : 0.426 4.103 1012 Z= 0.219 Chirality : 0.045 0.145 113 Planarity : 0.005 0.042 136 Dihedral : 3.503 10.261 104 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.41 (0.88), residues: 96 helix: None (None), residues: 0 sheet: 0.31 (0.90), residues: 36 loop : 0.37 (0.83), residues: 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.1795 time to fit residues: 2.5708 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 743 Z= 0.162 Angle : 0.441 4.131 1012 Z= 0.228 Chirality : 0.045 0.145 113 Planarity : 0.005 0.040 136 Dihedral : 3.592 11.248 104 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.88), residues: 96 helix: None (None), residues: 0 sheet: 0.33 (0.91), residues: 36 loop : 0.35 (0.83), residues: 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.0349 time to fit residues: 2.2643 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.160 Angle : 0.439 4.082 1012 Z= 0.226 Chirality : 0.045 0.145 113 Planarity : 0.005 0.041 136 Dihedral : 3.651 11.538 104 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.42 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.31 (0.91), residues: 36 loop : 0.38 (0.84), residues: 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.0438 time to fit residues: 2.3056 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 743 Z= 0.162 Angle : 0.444 4.127 1012 Z= 0.230 Chirality : 0.045 0.146 113 Planarity : 0.005 0.041 136 Dihedral : 3.658 10.820 104 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.39 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.30 (0.91), residues: 36 loop : 0.36 (0.84), residues: 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.2402 time to fit residues: 2.6952 Evaluate side-chains 2 residues out of total 76 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.057808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.054831 restraints weight = 22276.157| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.74 r_work: 0.4294 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.150 Angle : 0.430 4.062 1012 Z= 0.221 Chirality : 0.045 0.145 113 Planarity : 0.005 0.041 136 Dihedral : 3.510 10.064 104 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % 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: 0.37 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.29 (0.91), residues: 36 loop : 0.33 (0.84), residues: 60 =============================================================================== Job complete usr+sys time: 2179.97 seconds wall clock time: 38 minutes 56.88 seconds (2336.88 seconds total)