Starting phenix.real_space_refine on Thu Dec 7 16:36:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vzf_32227/12_2023/7vzf_32227.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1617 2.51 5 N 468 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ARG 115": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 876 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.77 Number of scatterers: 2628 At special positions: 0 Unit cell: (98.8, 100.88, 37.44, 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 9 16.00 O 534 8.00 N 468 7.00 C 1617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 574.7 milliseconds 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.689A pdb=" N VAL A 7 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 7 " --> pdb=" O LEU C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 41 removed outlier: 7.107A pdb=" N GLY B 33 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE B 35 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 36 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 37 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C 33 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 35 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 36 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY C 37 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'A' and resid 95 through 97 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.605A pdb=" N SER A 102 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N SER B 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 104 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 102 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER C 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 104 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AB1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AB2, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.538A pdb=" N ALA A 145 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 148 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY A 147 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE A 149 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N ALA B 152 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ILE A 151 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 145 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY B 147 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY C 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE B 149 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N ALA C 152 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE B 151 " --> pdb=" O ALA C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 26 hydrogen bonds defined for protein. 78 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: 0.56 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 886 1.33 - 1.45: 282 1.45 - 1.57: 1481 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 2658 Sorted by residual: bond pdb=" CB ASN A 19 " pdb=" CG ASN A 19 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.74e+00 bond pdb=" CB ASN C 19 " pdb=" CG ASN C 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.61e+00 bond pdb=" CB ASN B 19 " pdb=" CG ASN B 19 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.60e+00 bond pdb=" CB VAL B 118 " pdb=" CG1 VAL B 118 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CB VAL C 118 " pdb=" CG1 VAL C 118 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 ... (remaining 2653 not shown) Histogram of bond angle deviations from ideal: 102.35 - 108.66: 202 108.66 - 114.96: 1523 114.96 - 121.27: 1033 121.27 - 127.58: 797 127.58 - 133.88: 24 Bond angle restraints: 3579 Sorted by residual: angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 128.35 -12.05 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.18e+01 angle pdb=" CA LEU C 42 " pdb=" CB LEU C 42 " pdb=" CG LEU C 42 " ideal model delta sigma weight residual 116.30 128.30 -12.00 3.50e+00 8.16e-02 1.17e+01 angle pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" C ASP A 124 " ideal model delta sigma weight residual 110.80 117.81 -7.01 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N ASP C 124 " pdb=" CA ASP C 124 " pdb=" C ASP C 124 " ideal model delta sigma weight residual 110.80 117.78 -6.98 2.13e+00 2.20e-01 1.07e+01 ... (remaining 3574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1326 15.91 - 31.83: 177 31.83 - 47.74: 39 47.74 - 63.66: 3 63.66 - 79.57: 9 Dihedral angle restraints: 1554 sinusoidal: 585 harmonic: 969 Sorted by residual: dihedral pdb=" CA ILE B 18 " pdb=" C ILE B 18 " pdb=" N ASN B 19 " pdb=" CA ASN B 19 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE C 18 " pdb=" C ILE C 18 " pdb=" N ASN C 19 " pdb=" CA ASN C 19 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 18 " pdb=" C ILE A 18 " pdb=" N ASN A 19 " pdb=" CA ASN A 19 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 1551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 251 0.045 - 0.091: 110 0.091 - 0.136: 35 0.136 - 0.181: 12 0.181 - 0.226: 3 Chirality restraints: 411 Sorted by residual: chirality pdb=" CB VAL B 118 " pdb=" CA VAL B 118 " pdb=" CG1 VAL B 118 " pdb=" CG2 VAL B 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL C 118 " pdb=" CA VAL C 118 " pdb=" CG1 VAL C 118 " pdb=" CG2 VAL C 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 408 not shown) Planarity restraints: 474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE B 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE A 20 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 20 " 0.018 2.00e-02 2.50e+03 1.35e-02 3.18e+00 pdb=" CG PHE C 20 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 20 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 20 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 20 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 20 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 20 " 0.002 2.00e-02 2.50e+03 ... (remaining 471 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 36 2.56 - 3.14: 2294 3.14 - 3.73: 3944 3.73 - 4.31: 5191 4.31 - 4.90: 9443 Nonbonded interactions: 20908 Sorted by model distance: nonbonded pdb=" ND2 ASN A 53 " pdb=" O VAL C 14 " model vdw 1.971 2.520 nonbonded pdb=" OG1 THR A 137 " pdb=" O THR B 137 " model vdw 2.129 2.440 nonbonded pdb=" OG1 THR B 137 " pdb=" O THR C 137 " model vdw 2.160 2.440 nonbonded pdb=" ND1 HIS A 46 " pdb=" OE1 GLU B 100 " model vdw 2.204 2.520 nonbonded pdb=" N SER A 142 " pdb=" OG SER B 142 " model vdw 2.208 2.520 ... (remaining 20903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.500 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4319 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 : 0.009 0.051 2658 Z= 0.654 Angle : 1.063 12.048 3579 Z= 0.566 Chirality : 0.060 0.226 411 Planarity : 0.006 0.034 474 Dihedral : 16.233 79.572 942 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 38.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.50 % Favored : 73.50 % Rotamer: Outliers : 0.00 % Allowed : 19.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.56 (0.29), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.22), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 32 HIS 0.009 0.003 HIS B 43 PHE 0.030 0.004 PHE A 20 ARG 0.002 0.000 ARG B 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.8158 time to fit residues: 93.3408 Evaluate side-chains 35 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 48 HIS C 15 GLN C 48 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5144 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2658 Z= 0.316 Angle : 0.865 8.417 3579 Z= 0.458 Chirality : 0.053 0.148 411 Planarity : 0.004 0.024 474 Dihedral : 7.233 25.753 363 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.67 % Favored : 84.33 % Rotamer: Outliers : 15.25 % Allowed : 23.76 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.31), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 32 HIS 0.006 0.001 HIS C 48 PHE 0.018 0.003 PHE A 50 ARG 0.006 0.001 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 52 time to evaluate : 0.324 Fit side-chains outliers start: 43 outliers final: 10 residues processed: 90 average time/residue: 0.6695 time to fit residues: 62.6066 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 22 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0284 time to fit residues: 0.4624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 0.0050 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 48 HIS B 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.8421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2658 Z= 0.206 Angle : 0.741 7.150 3579 Z= 0.384 Chirality : 0.049 0.160 411 Planarity : 0.003 0.021 474 Dihedral : 5.759 21.257 363 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 10.99 % Allowed : 31.91 % Favored : 57.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.32), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 32 HIS 0.008 0.001 HIS B 46 PHE 0.009 0.002 PHE A 20 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 28 time to evaluate : 0.281 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 53 average time/residue: 0.8671 time to fit residues: 47.5521 Evaluate side-chains 38 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 24 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0262 time to fit residues: 0.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 48 HIS B 48 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 1.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2658 Z= 0.413 Angle : 0.968 11.620 3579 Z= 0.502 Chirality : 0.058 0.177 411 Planarity : 0.004 0.027 474 Dihedral : 7.275 26.076 363 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.94 % Favored : 80.06 % Rotamer: Outliers : 13.12 % Allowed : 31.56 % Favored : 55.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 32 HIS 0.008 0.002 HIS B 46 PHE 0.032 0.005 PHE B 20 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 30 time to evaluate : 0.311 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 59 average time/residue: 0.7469 time to fit residues: 45.7519 Evaluate side-chains 44 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 27 time to evaluate : 0.235 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.0829 time to fit residues: 0.6751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 1.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2658 Z= 0.229 Angle : 0.797 10.897 3579 Z= 0.399 Chirality : 0.050 0.163 411 Planarity : 0.003 0.012 474 Dihedral : 6.213 23.843 363 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.38 % Favored : 82.62 % Rotamer: Outliers : 10.28 % Allowed : 33.33 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.003 0.001 HIS A 120 PHE 0.019 0.003 PHE A 50 ARG 0.001 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 26 time to evaluate : 0.305 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 51 average time/residue: 0.7251 time to fit residues: 38.5211 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 20 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 0.4149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.5891 moved from start: 1.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2658 Z= 0.207 Angle : 0.767 9.100 3579 Z= 0.380 Chirality : 0.050 0.158 411 Planarity : 0.002 0.012 474 Dihedral : 5.843 22.250 363 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 7.80 % Allowed : 35.46 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.002 0.001 HIS A 120 PHE 0.015 0.002 PHE B 20 ARG 0.001 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 25 time to evaluate : 0.313 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 45 average time/residue: 0.8251 time to fit residues: 38.5262 Evaluate side-chains 38 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 24 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 0.4117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 1.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2658 Z= 0.327 Angle : 0.913 11.246 3579 Z= 0.458 Chirality : 0.053 0.173 411 Planarity : 0.003 0.026 474 Dihedral : 6.616 25.615 363 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.23 % Favored : 79.77 % Rotamer: Outliers : 7.45 % Allowed : 35.82 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 32 HIS 0.005 0.001 HIS A 120 PHE 0.028 0.005 PHE B 20 ARG 0.003 0.001 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 24 time to evaluate : 0.284 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 44 average time/residue: 0.7488 time to fit residues: 34.3747 Evaluate side-chains 36 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.0770 time to fit residues: 0.5062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 9 optimal weight: 0.0070 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 1.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2658 Z= 0.177 Angle : 0.727 7.873 3579 Z= 0.367 Chirality : 0.048 0.155 411 Planarity : 0.002 0.014 474 Dihedral : 5.601 21.747 363 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.67 % Favored : 84.33 % Rotamer: Outliers : 6.38 % Allowed : 38.30 % Favored : 55.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 32 HIS 0.004 0.001 HIS A 43 PHE 0.006 0.002 PHE A 50 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 0.307 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 50 average time/residue: 0.6449 time to fit residues: 33.7812 Evaluate side-chains 38 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 0.4028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 1.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2658 Z= 0.209 Angle : 0.770 9.334 3579 Z= 0.387 Chirality : 0.049 0.159 411 Planarity : 0.003 0.013 474 Dihedral : 5.543 20.993 363 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.95 % Favored : 82.05 % Rotamer: Outliers : 6.38 % Allowed : 37.23 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 32 HIS 0.004 0.001 HIS A 120 PHE 0.020 0.002 PHE A 50 ARG 0.001 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 28 time to evaluate : 0.292 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 45 average time/residue: 0.8751 time to fit residues: 40.8124 Evaluate side-chains 37 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.410 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 0.4228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 1.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2658 Z= 0.214 Angle : 0.778 9.257 3579 Z= 0.392 Chirality : 0.049 0.159 411 Planarity : 0.003 0.014 474 Dihedral : 5.558 20.615 363 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.95 % Favored : 82.05 % Rotamer: Outliers : 4.61 % Allowed : 38.65 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.004 0.001 HIS A 43 PHE 0.014 0.002 PHE B 20 ARG 0.001 0.000 ARG C 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 702 Ramachandran restraints generated. 351 Oldfield, 0 Emsley, 351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 0.333 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 37 average time/residue: 0.9850 time to fit residues: 37.7316 Evaluate side-chains 32 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 0.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 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 = 0.4882 r_free = 0.4882 target = 0.201078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.182747 restraints weight = 5208.185| |-----------------------------------------------------------------------------| r_work (start): 0.4674 rms_B_bonded: 2.89 r_work: 0.4592 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 1.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2658 Z= 0.291 Angle : 0.849 9.678 3579 Z= 0.426 Chirality : 0.051 0.167 411 Planarity : 0.003 0.014 474 Dihedral : 6.107 23.135 363 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.23 % Favored : 79.77 % Rotamer: Outliers : 4.96 % Allowed : 37.94 % Favored : 57.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.33), residues: 351 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 32 HIS 0.005 0.001 HIS A 43 PHE 0.024 0.003 PHE B 20 ARG 0.006 0.001 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.66 seconds wall clock time: 27 minutes 39.88 seconds (1659.88 seconds total)