Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qn7_18509/08_2024/8qn7_18509.cif" } resolution = 2.7 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 5 5.16 5 C 920 2.51 5 N 255 2.21 5 O 275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 1455 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 291 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 1.58, per 1000 atoms: 1.09 Number of scatterers: 1455 At special positions: 0 Unit cell: (82.584, 72.168, 29.76, 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 5 16.00 O 275 8.00 N 255 7.00 C 920 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: 1.31 Conformation dependent library (CDL) restraints added in 367.5 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 355 1.33 - 1.45: 410 1.45 - 1.58: 710 1.58 - 1.70: 0 1.70 - 1.82: 10 Bond restraints: 1485 Sorted by residual: bond pdb=" CA SER B 8 " pdb=" CB SER B 8 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.48e-02 4.57e+03 8.27e+00 bond pdb=" CA SER C 8 " pdb=" CB SER C 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.22e+00 bond pdb=" CA SER A 8 " pdb=" CB SER A 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.15e+00 bond pdb=" CA SER E 8 " pdb=" CB SER E 8 " ideal model delta sigma weight residual 1.530 1.487 0.042 1.48e-02 4.57e+03 8.15e+00 bond pdb=" CA SER D 8 " pdb=" CB SER D 8 " ideal model delta sigma weight residual 1.530 1.488 0.041 1.48e-02 4.57e+03 7.81e+00 ... (remaining 1480 not shown) Histogram of bond angle deviations from ideal: 99.48 - 105.98: 15 105.98 - 112.47: 651 112.47 - 118.97: 558 118.97 - 125.47: 736 125.47 - 131.96: 25 Bond angle restraints: 1985 Sorted by residual: angle pdb=" CA HIS E 13 " pdb=" CB HIS E 13 " pdb=" CG HIS E 13 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.69e+01 angle pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " pdb=" CG HIS A 13 " ideal model delta sigma weight residual 113.80 118.98 -5.18 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS C 13 " pdb=" CB HIS C 13 " pdb=" CG HIS C 13 " ideal model delta sigma weight residual 113.80 118.97 -5.17 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS B 13 " pdb=" CB HIS B 13 " pdb=" CG HIS B 13 " ideal model delta sigma weight residual 113.80 118.97 -5.17 1.00e+00 1.00e+00 2.68e+01 angle pdb=" CA HIS D 13 " pdb=" CB HIS D 13 " pdb=" CG HIS D 13 " ideal model delta sigma weight residual 113.80 118.96 -5.16 1.00e+00 1.00e+00 2.67e+01 ... (remaining 1980 not shown) Histogram of dihedral angle deviations from ideal: 0.04 - 11.62: 709 11.62 - 23.19: 76 23.19 - 34.77: 25 34.77 - 46.35: 15 46.35 - 57.93: 5 Dihedral angle restraints: 830 sinusoidal: 320 harmonic: 510 Sorted by residual: dihedral pdb=" CA GLU D 22 " pdb=" C GLU D 22 " pdb=" N ASP D 23 " pdb=" CA ASP D 23 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N ASP E 23 " pdb=" CA ASP E 23 " ideal model delta harmonic sigma weight residual 180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU A 22 " pdb=" C GLU A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 827 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 60 0.042 - 0.082: 54 0.082 - 0.123: 61 0.123 - 0.163: 15 0.163 - 0.204: 10 Chirality restraints: 200 Sorted by residual: chirality pdb=" CA HIS B 14 " pdb=" N HIS B 14 " pdb=" C HIS B 14 " pdb=" CB HIS B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA HIS E 14 " pdb=" N HIS E 14 " pdb=" C HIS E 14 " pdb=" CB HIS E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA HIS D 14 " pdb=" N HIS D 14 " pdb=" C HIS D 14 " pdb=" CB HIS D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 197 not shown) Planarity restraints: 265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 25 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C GLY E 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY E 25 " -0.010 2.00e-02 2.50e+03 pdb=" N SER E 26 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 25 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C GLY B 25 " 0.026 2.00e-02 2.50e+03 pdb=" O GLY B 25 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 26 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 25 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C GLY C 25 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY C 25 " 0.010 2.00e-02 2.50e+03 pdb=" N SER C 26 " 0.009 2.00e-02 2.50e+03 ... (remaining 262 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 779 3.04 - 3.50: 1239 3.50 - 3.97: 2210 3.97 - 4.43: 2481 4.43 - 4.90: 4512 Nonbonded interactions: 11221 Sorted by model distance: nonbonded pdb=" NZ LYS A 16 " pdb=" OE1 GLU B 11 " model vdw 2.570 3.120 nonbonded pdb=" OE1 GLU A 11 " pdb=" NZ LYS E 16 " model vdw 2.570 3.120 nonbonded pdb=" OE1 GLU C 11 " pdb=" NZ LYS D 16 " model vdw 2.570 3.120 nonbonded pdb=" N ALA B 30 " pdb=" O ALA B 30 " model vdw 2.652 2.496 nonbonded pdb=" N ALA C 30 " pdb=" O ALA C 30 " model vdw 2.653 2.496 ... (remaining 11216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 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 : 0.010 0.043 1485 Z= 0.647 Angle : 1.434 5.419 1985 Z= 0.986 Chirality : 0.087 0.204 200 Planarity : 0.010 0.058 265 Dihedral : 13.541 57.925 510 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.45 % Allowed : 0.00 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.33), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.006 HIS D 13 PHE 0.016 0.007 PHE A 19 TYR 0.006 0.003 TYR E 10 ARG 0.006 0.003 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.151 Fit side-chains REVERT: C 3 GLU cc_start: 0.8908 (tt0) cc_final: 0.8218 (tm-30) REVERT: E 3 GLU cc_start: 0.8847 (tt0) cc_final: 0.8167 (tm-30) outliers start: 5 outliers final: 0 residues processed: 52 average time/residue: 1.3310 time to fit residues: 70.0987 Evaluate side-chains 40 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS E 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1485 Z= 0.196 Angle : 0.626 4.164 1985 Z= 0.329 Chirality : 0.051 0.112 200 Planarity : 0.002 0.017 265 Dihedral : 5.578 16.522 195 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.69 % Allowed : 5.52 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.37), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 13 PHE 0.008 0.002 PHE D 19 TYR 0.003 0.001 TYR A 10 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.166 Fit side-chains REVERT: A 3 GLU cc_start: 0.8774 (tt0) cc_final: 0.8480 (mt-10) REVERT: B 3 GLU cc_start: 0.8916 (tt0) cc_final: 0.8554 (mt-10) REVERT: C 3 GLU cc_start: 0.8916 (tt0) cc_final: 0.8685 (mt-10) REVERT: D 3 GLU cc_start: 0.8773 (tt0) cc_final: 0.8358 (mt-10) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 1.4983 time to fit residues: 66.6998 Evaluate side-chains 44 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 1485 Z= 0.206 Angle : 0.595 4.081 1985 Z= 0.310 Chirality : 0.050 0.115 200 Planarity : 0.002 0.022 265 Dihedral : 5.544 16.598 195 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.38 % Allowed : 8.97 % Favored : 89.66 % 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: -3.09 (0.39), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.30), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 13 PHE 0.009 0.001 PHE D 19 TYR 0.007 0.001 TYR C 10 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.160 Fit side-chains REVERT: A 3 GLU cc_start: 0.8744 (tt0) cc_final: 0.8393 (mt-10) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 1.4648 time to fit residues: 65.2378 Evaluate side-chains 43 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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: 0.9061 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1485 Z= 0.138 Angle : 0.494 3.459 1985 Z= 0.260 Chirality : 0.049 0.118 200 Planarity : 0.001 0.011 265 Dihedral : 5.201 16.031 195 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.07 % Allowed : 11.03 % Favored : 86.90 % 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: -3.08 (0.40), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.007 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.167 Fit side-chains REVERT: A 3 GLU cc_start: 0.8745 (tt0) cc_final: 0.8412 (mt-10) outliers start: 3 outliers final: 0 residues processed: 43 average time/residue: 1.5522 time to fit residues: 67.5151 Evaluate side-chains 42 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1485 Z= 0.178 Angle : 0.540 3.749 1985 Z= 0.283 Chirality : 0.050 0.117 200 Planarity : 0.002 0.013 265 Dihedral : 5.270 16.277 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.45 % Allowed : 11.03 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 13 PHE 0.008 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.168 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 1.5848 time to fit residues: 73.6898 Evaluate side-chains 42 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.9078 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1485 Z= 0.186 Angle : 0.553 3.829 1985 Z= 0.288 Chirality : 0.050 0.117 200 Planarity : 0.002 0.016 265 Dihedral : 5.263 16.530 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.45 % Allowed : 10.34 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.008 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.165 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 48 average time/residue: 1.6986 time to fit residues: 82.3767 Evaluate side-chains 42 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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: 0.9086 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 1485 Z= 0.233 Angle : 0.615 4.266 1985 Z= 0.318 Chirality : 0.051 0.117 200 Planarity : 0.002 0.021 265 Dihedral : 5.392 17.050 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.45 % Allowed : 9.66 % Favored : 86.90 % 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: -3.22 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 13 PHE 0.010 0.002 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.179 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 1.6472 time to fit residues: 76.5823 Evaluate side-chains 44 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.007 1485 Z= 0.081 Angle : 0.418 3.236 1985 Z= 0.225 Chirality : 0.049 0.120 200 Planarity : 0.001 0.006 265 Dihedral : 4.733 15.453 195 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.38 % Allowed : 12.41 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 13 PHE 0.004 0.001 PHE D 19 TYR 0.006 0.001 TYR E 10 ARG 0.003 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.124 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 1.1485 time to fit residues: 49.9368 Evaluate side-chains 40 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1485 Z= 0.151 Angle : 0.502 3.596 1985 Z= 0.264 Chirality : 0.050 0.119 200 Planarity : 0.002 0.014 265 Dihedral : 5.004 15.836 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.38 % Allowed : 13.10 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.007 0.001 PHE D 19 TYR 0.004 0.001 TYR E 10 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.162 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 1.5793 time to fit residues: 68.6441 Evaluate side-chains 41 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.0470 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 overall best weight: 2.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.010 1485 Z= 0.118 Angle : 0.464 3.299 1985 Z= 0.246 Chirality : 0.049 0.119 200 Planarity : 0.001 0.009 265 Dihedral : 4.853 15.536 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.69 % Allowed : 14.48 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.42), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.32), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.006 0.001 PHE D 19 TYR 0.005 0.001 TYR E 10 ARG 0.001 0.000 ARG B 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.173 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 1.6595 time to fit residues: 67.1310 Evaluate side-chains 40 residues out of total 145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118257 restraints weight = 1534.044| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.18 r_work: 0.3570 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1485 Z= 0.186 Angle : 0.548 3.892 1985 Z= 0.288 Chirality : 0.050 0.118 200 Planarity : 0.002 0.016 265 Dihedral : 5.111 16.099 195 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.69 % Allowed : 14.48 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.41), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 13 PHE 0.009 0.001 PHE D 19 TYR 0.006 0.001 TYR E 10 ARG 0.001 0.000 ARG A 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1538.34 seconds wall clock time: 30 minutes 41.89 seconds (1841.89 seconds total)