Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:54:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxw_23577/11_2022/7lxw_23577.pdb" } resolution = 2.8 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2524 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 737 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 945 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.00, per 1000 atoms: 0.79 Number of scatterers: 2524 At special positions: 0 Unit cell: (78.848, 61.824, 68.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 482 8.00 N 429 7.00 C 1602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG C 1 " - " FUC C 2 " NAG-ASN " NAG B 1 " - " ASN A 17 " " NAG C 1 " - " ASN A 149 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 421.7 milliseconds 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 580 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.2% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 10 removed outlier: 5.999A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.230A pdb=" N GLY H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.230A pdb=" N GLY H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 131 removed outlier: 5.722A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 12.871A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.189A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 231 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: 0.70 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: 1.20 - 1.32: 502 1.32 - 1.45: 667 1.45 - 1.57: 1394 1.57 - 1.69: 4 1.69 - 1.81: 14 Bond restraints: 2581 Sorted by residual: bond pdb=" CB ILE A 100 " pdb=" CG1 ILE A 100 " ideal model delta sigma weight residual 1.530 1.591 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.468 -0.033 1.10e-02 8.26e+03 8.98e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.435 1.465 -0.030 1.10e-02 8.26e+03 7.57e+00 bond pdb=" NE ARG L 29 " pdb=" CZ ARG L 29 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.63e+00 bond pdb=" CD GLU A 132 " pdb=" OE1 GLU A 132 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.39e+00 ... (remaining 2576 not shown) Histogram of bond angle deviations from ideal: 101.09 - 107.64: 96 107.64 - 114.19: 1436 114.19 - 120.75: 1074 120.75 - 127.30: 866 127.30 - 133.86: 29 Bond angle restraints: 3501 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.20e-01 1.93e+00 9.02e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.55e+01 angle pdb=" C ILE L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 119.78 126.70 -6.92 1.03e+00 9.43e-01 4.52e+01 angle pdb=" C PRO L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.32 126.97 -7.65 1.14e+00 7.69e-01 4.51e+01 angle pdb=" C ALA L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.78 126.13 -6.35 1.03e+00 9.43e-01 3.80e+01 ... (remaining 3496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1447 17.97 - 35.93: 40 35.93 - 53.90: 6 53.90 - 71.86: 4 71.86 - 89.83: 2 Dihedral angle restraints: 1499 sinusoidal: 597 harmonic: 902 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.15 41.85 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CG ARG L 60 " pdb=" CD ARG L 60 " pdb=" NE ARG L 60 " pdb=" CZ ARG L 60 " ideal model delta sinusoidal sigma weight residual 90.00 134.38 -44.38 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 1496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 284 0.063 - 0.126: 88 0.126 - 0.190: 15 0.190 - 0.253: 5 0.253 - 0.316: 6 Chirality restraints: 398 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.37e+01 chirality pdb=" C1 FUC C 2 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 2 " pdb=" O5 FUC C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 7.96e+00 ... (remaining 395 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 109 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C PHE H 109 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE H 109 " -0.012 2.00e-02 2.50e+03 pdb=" N THR H 110 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.025 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" CG TRP H 47 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 95 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C PHE H 95 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE H 95 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS H 96 " 0.011 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1574 3.05 - 3.52: 2182 3.52 - 3.98: 4179 3.98 - 4.44: 4778 4.44 - 4.90: 7723 Nonbonded interactions: 20436 Sorted by model distance: nonbonded pdb=" N THR H 110 " pdb=" O THR H 110 " model vdw 2.593 2.496 nonbonded pdb=" N SER L 62 " pdb=" O SER L 62 " model vdw 2.619 2.496 nonbonded pdb=" O SER L 75 " pdb=" C ARG L 76 " model vdw 2.629 3.270 nonbonded pdb=" O ASP A 138 " pdb=" CB ASP A 138 " model vdw 2.642 2.752 nonbonded pdb=" N GLY H 115 " pdb=" O GLY H 115 " model vdw 2.643 2.496 ... (remaining 20431 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1602 2.51 5 N 429 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.570 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: 0.010 Extract box with map and model: 40.440 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.050 Process input model: 17.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.067 2581 Z= 0.746 Angle : 1.196 7.653 3501 Z= 0.834 Chirality : 0.073 0.316 398 Planarity : 0.005 0.019 438 Dihedral : 10.028 89.828 910 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.97 (0.45), residues: 299 helix: None (None), residues: 0 sheet: 0.66 (0.41), residues: 129 loop : 0.81 (0.46), residues: 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.0119 time to fit residues: 76.8188 Evaluate side-chains 46 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.0970 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.0270 chunk 15 optimal weight: 0.0980 chunk 12 optimal weight: 0.0970 chunk 24 optimal weight: 0.0770 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 0.0670 chunk 18 optimal weight: 0.0870 chunk 28 optimal weight: 0.0970 overall best weight: 0.0670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN A 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 2581 Z= 0.205 Angle : 0.590 10.546 3501 Z= 0.328 Chirality : 0.047 0.245 398 Planarity : 0.004 0.026 438 Dihedral : 4.707 23.260 374 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.34 % Favored : 98.33 % Rotamer Outliers : 4.56 % 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: 1.10 (0.47), residues: 299 helix: None (None), residues: 0 sheet: 0.85 (0.43), residues: 131 loop : 0.79 (0.48), residues: 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.278 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 66 average time/residue: 0.8583 time to fit residues: 58.4906 Evaluate side-chains 57 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0320 time to fit residues: 0.4864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 25 optimal weight: 0.3980 chunk 27 optimal weight: 0.0570 chunk 9 optimal weight: 0.0980 chunk 22 optimal weight: 0.0670 overall best weight: 0.0752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2581 Z= 0.169 Angle : 0.504 5.683 3501 Z= 0.281 Chirality : 0.046 0.308 398 Planarity : 0.004 0.026 438 Dihedral : 4.432 18.545 374 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 4.18 % 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: 1.01 (0.48), residues: 299 helix: None (None), residues: 0 sheet: 0.73 (0.43), residues: 129 loop : 0.79 (0.49), residues: 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.325 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 0.7039 time to fit residues: 49.0504 Evaluate side-chains 57 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0279 time to fit residues: 0.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 24 optimal weight: 0.0770 overall best weight: 0.1112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN L 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2581 Z= 0.195 Angle : 0.495 5.271 3501 Z= 0.274 Chirality : 0.044 0.186 398 Planarity : 0.004 0.026 438 Dihedral : 4.495 19.061 374 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.48), residues: 299 helix: None (None), residues: 0 sheet: 0.67 (0.44), residues: 121 loop : 0.76 (0.48), residues: 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.288 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 62 average time/residue: 0.7676 time to fit residues: 49.2998 Evaluate side-chains 56 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0233 time to fit residues: 0.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.0070 chunk 15 optimal weight: 0.0370 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 5 optimal weight: 0.6980 overall best weight: 0.0552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 2581 Z= 0.145 Angle : 0.478 4.981 3501 Z= 0.262 Chirality : 0.045 0.242 398 Planarity : 0.003 0.027 438 Dihedral : 4.359 17.810 374 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 2.28 % 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: 0.95 (0.48), residues: 299 helix: None (None), residues: 0 sheet: 0.65 (0.44), residues: 121 loop : 0.78 (0.49), residues: 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.265 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 0.8209 time to fit residues: 52.6529 Evaluate side-chains 56 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1940 time to fit residues: 0.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 3 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 2581 Z= 0.349 Angle : 0.573 5.296 3501 Z= 0.312 Chirality : 0.047 0.254 398 Planarity : 0.005 0.047 438 Dihedral : 4.704 20.019 374 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 4.18 % 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: 0.68 (0.50), residues: 299 helix: None (None), residues: 0 sheet: 0.29 (0.42), residues: 135 loop : 0.79 (0.53), residues: 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.307 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.8276 time to fit residues: 53.0590 Evaluate side-chains 62 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.0696 time to fit residues: 0.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 0.0010 chunk 25 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 0.0870 chunk 11 optimal weight: 0.0670 chunk 17 optimal weight: 0.1980 chunk 9 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 overall best weight: 0.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 2581 Z= 0.159 Angle : 0.481 4.726 3501 Z= 0.266 Chirality : 0.045 0.265 398 Planarity : 0.004 0.034 438 Dihedral : 4.439 18.264 374 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 3.04 % 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: 0.76 (0.50), residues: 299 helix: None (None), residues: 0 sheet: 0.47 (0.44), residues: 129 loop : 0.71 (0.52), residues: 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.299 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.8192 time to fit residues: 50.0593 Evaluate side-chains 56 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0276 time to fit residues: 0.4549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 0.1980 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 2581 Z= 0.281 Angle : 0.546 5.004 3501 Z= 0.300 Chirality : 0.047 0.278 398 Planarity : 0.005 0.045 438 Dihedral : 4.626 19.254 374 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.66 % 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: 0.49 (0.50), residues: 299 helix: None (None), residues: 0 sheet: 0.27 (0.43), residues: 132 loop : 0.54 (0.52), residues: 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.290 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.8436 time to fit residues: 51.4132 Evaluate side-chains 59 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0926 time to fit residues: 0.6250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.0870 chunk 28 optimal weight: 0.0370 chunk 24 optimal weight: 0.0670 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 0.0870 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 overall best weight: 0.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 2581 Z= 0.202 Angle : 0.505 4.620 3501 Z= 0.279 Chirality : 0.046 0.291 398 Planarity : 0.004 0.043 438 Dihedral : 4.511 18.101 374 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.49), residues: 299 helix: None (None), residues: 0 sheet: 0.31 (0.44), residues: 129 loop : 0.46 (0.51), residues: 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.306 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.7078 time to fit residues: 44.9092 Evaluate side-chains 57 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.0570 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 10 optimal weight: 0.0870 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 0.0570 chunk 21 optimal weight: 0.0970 chunk 1 optimal weight: 0.1980 overall best weight: 0.0770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 2581 Z= 0.173 Angle : 0.504 4.905 3501 Z= 0.277 Chirality : 0.046 0.292 398 Planarity : 0.004 0.041 438 Dihedral : 4.423 17.156 374 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.50), residues: 299 helix: None (None), residues: 0 sheet: 0.28 (0.44), residues: 132 loop : 0.56 (0.52), residues: 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 598 Ramachandran restraints generated. 299 Oldfield, 0 Emsley, 299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.295 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.7640 time to fit residues: 48.3861 Evaluate side-chains 58 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 12 optimal weight: 0.0980 chunk 11 optimal weight: 0.0770 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 0.0670 overall best weight: 0.1074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN L 68 ASN L 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107468 restraints weight = 3742.502| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.00 r_work: 0.3338 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3323 rms_B_bonded: 1.86 restraints_weight: 0.1250 r_work: 0.3315 rms_B_bonded: 1.91 restraints_weight: 0.0625 r_work: 0.3306 rms_B_bonded: 1.98 restraints_weight: 0.0312 r_work: 0.3297 rms_B_bonded: 2.08 restraints_weight: 0.0156 r_work: 0.3288 rms_B_bonded: 2.19 restraints_weight: 0.0078 r_work: 0.3278 rms_B_bonded: 2.32 restraints_weight: 0.0039 r_work: 0.3268 rms_B_bonded: 2.47 restraints_weight: 0.0020 r_work: 0.3258 rms_B_bonded: 2.64 restraints_weight: 0.0010 r_work: 0.3247 rms_B_bonded: 2.82 restraints_weight: 0.0005 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.0002 r_work: 0.3222 rms_B_bonded: 3.26 restraints_weight: 0.0001 r_work: 0.3209 rms_B_bonded: 3.52 restraints_weight: 0.0001 r_work: 0.3195 rms_B_bonded: 3.80 restraints_weight: 0.0000 r_work: 0.3180 rms_B_bonded: 4.10 restraints_weight: 0.0000 r_work: 0.3164 rms_B_bonded: 4.44 restraints_weight: 0.0000 r_work: 0.3148 rms_B_bonded: 4.81 restraints_weight: 0.0000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 2581 Z= 0.210 Angle : 0.527 5.372 3501 Z= 0.289 Chirality : 0.046 0.293 398 Planarity : 0.005 0.041 438 Dihedral : 4.469 17.261 374 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.50), residues: 299 helix: None (None), residues: 0 sheet: 0.28 (0.43), residues: 132 loop : 0.57 (0.53), residues: 167 =============================================================================== Job complete usr+sys time: 2064.83 seconds wall clock time: 37 minutes 18.01 seconds (2238.01 seconds total)