Starting phenix.real_space_refine on Sun Mar 10 19:06:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/03_2024/7yr6_34047.pdb" } resolution = 4.8 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= 0.004 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 8 5.16 5 C 2197 2.51 5 N 797 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 7": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4248 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 426 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2547 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 7, 'rna3p_pur': 52, 'rna3p_pyr': 39} Link IDs: {'rna2p': 26, 'rna3p': 91} Time building chain proxies: 3.09, per 1000 atoms: 0.73 Number of scatterers: 4248 At special positions: 0 Unit cell: (84.15, 91.8, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 118 15.00 O 1128 8.00 N 797 7.00 C 2197 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: 2.37 Conformation dependent library (CDL) restraints added in 382.6 milliseconds 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 398 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 3 sheets defined 14.1% alpha, 14.1% beta 30 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'B' and resid 45 through 49 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.787A pdb=" N GLY D 33 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 26 removed outlier: 5.104A pdb=" N VAL C 22 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 33 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 30 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 6 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.744A pdb=" N THR B 21 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 33 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG B 31 " --> pdb=" O LEU B 23 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 2.51 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: 672 1.33 - 1.45: 1678 1.45 - 1.57: 1962 1.57 - 1.69: 235 1.69 - 1.80: 16 Bond restraints: 4563 Sorted by residual: bond pdb=" O3' C A 15 " pdb=" P G A 16 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.50e-02 4.44e+03 1.54e+01 bond pdb=" O3' G A 57 " pdb=" P A A 58 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O3' C A 61 " pdb=" P C A 62 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.50e-02 4.44e+03 8.77e+00 bond pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" O3' A A 63 " pdb=" P U A 64 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.28e+00 ... (remaining 4558 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.06: 686 106.06 - 112.80: 2542 112.80 - 119.55: 1447 119.55 - 126.30: 1694 126.30 - 133.05: 387 Bond angle restraints: 6756 Sorted by residual: angle pdb=" O3' C A 61 " pdb=" C3' C A 61 " pdb=" C2' C A 61 " ideal model delta sigma weight residual 109.50 119.51 -10.01 1.50e+00 4.44e-01 4.46e+01 angle pdb=" N ILE D 47 " pdb=" CA ILE D 47 " pdb=" C ILE D 47 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" C ILE E 47 " pdb=" N TYR E 48 " pdb=" CA TYR E 48 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" O3' G A 81 " pdb=" C3' G A 81 " pdb=" C2' G A 81 " ideal model delta sigma weight residual 109.50 115.96 -6.46 1.50e+00 4.44e-01 1.85e+01 angle pdb=" N LEU E 23 " pdb=" CA LEU E 23 " pdb=" C LEU E 23 " ideal model delta sigma weight residual 110.88 116.23 -5.35 1.28e+00 6.10e-01 1.75e+01 ... (remaining 6751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 2492 35.86 - 71.71: 367 71.71 - 107.57: 49 107.57 - 143.42: 3 143.42 - 179.28: 2 Dihedral angle restraints: 2913 sinusoidal: 2295 harmonic: 618 Sorted by residual: dihedral pdb=" O4' U A 60 " pdb=" C1' U A 60 " pdb=" N1 U A 60 " pdb=" C2 U A 60 " ideal model delta sinusoidal sigma weight residual 200.00 53.25 146.75 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' G A 39 " pdb=" C1' G A 39 " pdb=" N9 G A 39 " pdb=" C4 G A 39 " ideal model delta sinusoidal sigma weight residual 68.00 153.16 -85.16 1 1.70e+01 3.46e-03 3.04e+01 dihedral pdb=" CA VAL D 18 " pdb=" C VAL D 18 " pdb=" N THR D 19 " pdb=" CA THR D 19 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 2910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 822 0.105 - 0.210: 46 0.210 - 0.316: 6 0.316 - 0.421: 1 0.421 - 0.526: 1 Chirality restraints: 876 Sorted by residual: chirality pdb=" C3' C A 61 " pdb=" C4' C A 61 " pdb=" O3' C A 61 " pdb=" C2' C A 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB ILE C 32 " pdb=" CA ILE C 32 " pdb=" CG1 ILE C 32 " pdb=" CG2 ILE C 32 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" P G A 57 " pdb=" OP1 G A 57 " pdb=" OP2 G A 57 " pdb=" O5' G A 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 873 not shown) Planarity restraints: 413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 35 " -0.022 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" N9 G A 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A 35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A 35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 35 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 91 " 0.021 2.00e-02 2.50e+03 1.08e-02 2.63e+00 pdb=" N1 U A 91 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U A 91 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U A 91 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U A 91 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U A 91 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U A 91 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A 91 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 48 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C TYR E 48 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR E 48 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN E 49 " -0.009 2.00e-02 2.50e+03 ... (remaining 410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1060 2.81 - 3.33: 3678 3.33 - 3.86: 8638 3.86 - 4.38: 9229 4.38 - 4.90: 12472 Nonbonded interactions: 35077 Sorted by model distance: nonbonded pdb=" O2' G A 50 " pdb=" O4' G A 51 " model vdw 2.291 2.440 nonbonded pdb=" O2' A A 41 " pdb=" O5' G A 43 " model vdw 2.326 2.440 nonbonded pdb=" O GLU B 10 " pdb=" OG1 THR B 21 " model vdw 2.342 2.440 nonbonded pdb=" O VAL E 40 " pdb=" N1 G A 10 " model vdw 2.370 2.520 nonbonded pdb=" O VAL B 42 " pdb=" N2 G A 39 " model vdw 2.397 2.520 ... (remaining 35072 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 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 55)) selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O )) or resid 25 through 55)) selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 55)) } 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 group one per residue 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: 0.470 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: 2.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.560 Find NCS groups from input model: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.004 0.059 4563 Z= 0.260 Angle : 0.883 10.014 6756 Z= 0.497 Chirality : 0.055 0.526 876 Planarity : 0.004 0.028 413 Dihedral : 26.030 179.280 2515 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 3.30 % Allowed : 12.09 % Favored : 84.62 % 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: -5.39 (0.42), residues: 212 helix: -3.34 (0.76), residues: 24 sheet: -3.13 (0.95), residues: 29 loop : -4.07 (0.34), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 43 TYR 0.008 0.001 TYR B 48 ARG 0.005 0.001 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9402 (tmm) cc_final: 0.9171 (tmm) REVERT: E 46 GLU cc_start: 0.9307 (tp30) cc_final: 0.8712 (tp30) REVERT: E 47 ILE cc_start: 0.8852 (mt) cc_final: 0.8353 (mp) REVERT: C 43 HIS cc_start: 0.9032 (m-70) cc_final: 0.8789 (m90) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.2460 time to fit residues: 23.8406 Evaluate side-chains 59 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS B 28 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4563 Z= 0.177 Angle : 0.591 5.315 6756 Z= 0.314 Chirality : 0.036 0.177 876 Planarity : 0.004 0.026 413 Dihedral : 26.711 178.385 2095 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.34 % Favored : 80.66 % Rotamer: Outliers : 0.55 % Allowed : 7.69 % Favored : 91.76 % 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: -5.07 (0.48), residues: 212 helix: -2.71 (0.87), residues: 28 sheet: -2.85 (1.08), residues: 22 loop : -3.93 (0.40), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 43 TYR 0.005 0.001 TYR E 48 ARG 0.008 0.001 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9438 (tmm) cc_final: 0.9057 (tmm) REVERT: E 44 ARG cc_start: 0.8296 (mtp180) cc_final: 0.8091 (mtt-85) REVERT: E 47 ILE cc_start: 0.8669 (mt) cc_final: 0.8360 (mp) REVERT: C 31 ARG cc_start: 0.9036 (mtt180) cc_final: 0.8654 (ttt180) REVERT: B 1 MET cc_start: 0.7579 (mpp) cc_final: 0.7075 (mpp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2521 time to fit residues: 18.9744 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4563 Z= 0.333 Angle : 0.800 6.087 6756 Z= 0.416 Chirality : 0.044 0.262 876 Planarity : 0.006 0.047 413 Dihedral : 27.420 176.289 2095 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 44.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.06 % Favored : 75.94 % Rotamer: Outliers : 1.10 % Allowed : 12.64 % Favored : 86.26 % 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: -5.16 (0.51), residues: 212 helix: -2.83 (0.80), residues: 28 sheet: -2.79 (1.10), residues: 22 loop : -4.01 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS E 43 TYR 0.004 0.001 TYR D 48 ARG 0.005 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 7 ARG cc_start: 0.9335 (tpp-160) cc_final: 0.8988 (tpp80) REVERT: E 13 MET cc_start: 0.9475 (tmm) cc_final: 0.9172 (tmm) REVERT: E 44 ARG cc_start: 0.8890 (mtp180) cc_final: 0.8384 (mtt180) REVERT: E 47 ILE cc_start: 0.8902 (mt) cc_final: 0.8602 (mp) REVERT: C 2 LEU cc_start: 0.8064 (mm) cc_final: 0.7776 (mm) outliers start: 2 outliers final: 0 residues processed: 59 average time/residue: 0.2328 time to fit residues: 16.0957 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4563 Z= 0.268 Angle : 0.712 6.299 6756 Z= 0.373 Chirality : 0.041 0.208 876 Planarity : 0.004 0.032 413 Dihedral : 27.369 175.356 2095 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 38.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Rotamer: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.01 % 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: -4.95 (0.52), residues: 212 helix: -2.54 (0.81), residues: 28 sheet: -3.04 (1.04), residues: 22 loop : -3.81 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS B 43 TYR 0.007 0.001 TYR C 48 ARG 0.008 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9137 (ttp) cc_final: 0.8457 (tmm) REVERT: E 13 MET cc_start: 0.9469 (tmm) cc_final: 0.9174 (tmm) REVERT: E 44 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8215 (mtt-85) REVERT: E 47 ILE cc_start: 0.8829 (mt) cc_final: 0.8545 (mp) REVERT: C 2 LEU cc_start: 0.8165 (mm) cc_final: 0.7950 (mm) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.2532 time to fit residues: 17.0136 Evaluate side-chains 48 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4563 Z= 0.261 Angle : 0.711 6.307 6756 Z= 0.374 Chirality : 0.041 0.218 876 Planarity : 0.005 0.036 413 Dihedral : 27.425 176.069 2095 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 38.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % 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: -4.78 (0.52), residues: 212 helix: -2.15 (0.90), residues: 22 sheet: -3.06 (1.01), residues: 22 loop : -3.69 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 43 TYR 0.020 0.002 TYR B 48 ARG 0.006 0.001 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9191 (ttp) cc_final: 0.8497 (tmm) REVERT: E 13 MET cc_start: 0.9483 (tmm) cc_final: 0.9192 (tmm) REVERT: E 44 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8279 (mtt-85) REVERT: E 47 ILE cc_start: 0.8880 (mt) cc_final: 0.8618 (mp) REVERT: D 48 TYR cc_start: 0.9215 (t80) cc_final: 0.8931 (t80) REVERT: C 2 LEU cc_start: 0.8221 (mm) cc_final: 0.8015 (mm) REVERT: B 7 ARG cc_start: 0.8584 (ttt180) cc_final: 0.8206 (ttt180) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2553 time to fit residues: 17.7030 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 0.0470 chunk 21 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4563 Z= 0.198 Angle : 0.654 6.216 6756 Z= 0.347 Chirality : 0.039 0.208 876 Planarity : 0.004 0.026 413 Dihedral : 27.245 174.326 2095 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -4.77 (0.51), residues: 212 helix: -2.70 (0.81), residues: 22 sheet: -2.76 (1.03), residues: 22 loop : -3.64 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 43 TYR 0.005 0.001 TYR E 48 ARG 0.004 0.001 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9155 (ttp) cc_final: 0.8496 (tmm) REVERT: E 2 LEU cc_start: 0.9497 (tp) cc_final: 0.9279 (tp) REVERT: E 13 MET cc_start: 0.9494 (tmm) cc_final: 0.9145 (tmm) REVERT: E 44 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8245 (mtt-85) REVERT: E 47 ILE cc_start: 0.8901 (mt) cc_final: 0.8631 (mp) REVERT: D 48 TYR cc_start: 0.9356 (t80) cc_final: 0.9142 (t80) REVERT: C 1 MET cc_start: 0.4005 (mtt) cc_final: 0.2953 (mtt) REVERT: C 2 LEU cc_start: 0.8135 (mm) cc_final: 0.7929 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2409 time to fit residues: 17.6422 Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4563 Z= 0.202 Angle : 0.649 6.174 6756 Z= 0.343 Chirality : 0.040 0.205 876 Planarity : 0.004 0.018 413 Dihedral : 27.211 174.488 2095 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 33.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.17 % Favored : 77.83 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % 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: -4.70 (0.52), residues: 212 helix: -3.02 (0.79), residues: 22 sheet: -2.35 (1.15), residues: 22 loop : -3.59 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 43 TYR 0.006 0.001 TYR C 48 ARG 0.004 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9173 (ttp) cc_final: 0.8520 (tmm) REVERT: E 2 LEU cc_start: 0.9478 (tp) cc_final: 0.9267 (tp) REVERT: E 13 MET cc_start: 0.9502 (tmm) cc_final: 0.9157 (tmm) REVERT: E 44 ARG cc_start: 0.8785 (mtp180) cc_final: 0.8490 (mtt180) REVERT: E 47 ILE cc_start: 0.8875 (mt) cc_final: 0.8212 (mp) REVERT: E 50 ARG cc_start: 0.9487 (pmt170) cc_final: 0.9162 (pmt170) REVERT: D 48 TYR cc_start: 0.9284 (t80) cc_final: 0.8999 (t80) REVERT: C 1 MET cc_start: 0.4032 (mtt) cc_final: 0.3130 (mtt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2485 time to fit residues: 18.1756 Evaluate side-chains 53 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4563 Z= 0.388 Angle : 0.891 7.302 6756 Z= 0.465 Chirality : 0.049 0.320 876 Planarity : 0.006 0.039 413 Dihedral : 27.866 175.661 2095 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 54.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.89 % Favored : 73.11 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -5.06 (0.51), residues: 212 helix: -3.29 (0.77), residues: 22 sheet: -2.87 (1.42), residues: 12 loop : -3.80 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS E 43 TYR 0.011 0.002 TYR D 48 ARG 0.009 0.001 ARG B 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9280 (ttp) cc_final: 0.8920 (tmm) REVERT: E 44 ARG cc_start: 0.9035 (mtp180) cc_final: 0.8376 (mtt-85) REVERT: E 46 GLU cc_start: 0.9459 (tp30) cc_final: 0.8946 (tp30) REVERT: E 47 ILE cc_start: 0.8984 (mt) cc_final: 0.8414 (mt) REVERT: E 50 ARG cc_start: 0.9521 (pmt170) cc_final: 0.9268 (pmt170) REVERT: D 48 TYR cc_start: 0.9369 (t80) cc_final: 0.9126 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2462 time to fit residues: 16.0619 Evaluate side-chains 45 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4563 Z= 0.321 Angle : 0.809 7.422 6756 Z= 0.424 Chirality : 0.045 0.284 876 Planarity : 0.006 0.053 413 Dihedral : 27.728 175.203 2095 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 46.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -5.06 (0.51), residues: 212 helix: -3.29 (0.78), residues: 22 sheet: -2.84 (1.40), residues: 12 loop : -3.81 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS B 43 TYR 0.012 0.002 TYR C 48 ARG 0.006 0.001 ARG C 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9258 (ttp) cc_final: 0.8855 (tmm) REVERT: E 44 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8353 (mtt-85) REVERT: E 46 GLU cc_start: 0.9459 (tp30) cc_final: 0.8930 (tp30) REVERT: E 47 ILE cc_start: 0.9026 (mt) cc_final: 0.8475 (mt) REVERT: E 50 ARG cc_start: 0.9528 (pmt170) cc_final: 0.9254 (pmt170) REVERT: D 48 TYR cc_start: 0.9315 (t80) cc_final: 0.9088 (t80) REVERT: C 1 MET cc_start: 0.4151 (mtt) cc_final: 0.3171 (mtt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2535 time to fit residues: 18.0403 Evaluate side-chains 44 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4563 Z= 0.269 Angle : 0.745 6.141 6756 Z= 0.394 Chirality : 0.043 0.256 876 Planarity : 0.005 0.027 413 Dihedral : 27.582 174.827 2095 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 41.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.52), residues: 212 helix: -3.03 (0.88), residues: 22 sheet: -2.86 (1.42), residues: 12 loop : -3.72 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS B 43 TYR 0.033 0.003 TYR B 48 ARG 0.005 0.001 ARG C 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 424 Ramachandran restraints generated. 212 Oldfield, 0 Emsley, 212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9242 (ttp) cc_final: 0.8864 (tmm) REVERT: E 44 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8330 (mtt-85) REVERT: D 48 TYR cc_start: 0.9316 (t80) cc_final: 0.9094 (t80) REVERT: C 1 MET cc_start: 0.3982 (mtt) cc_final: 0.3073 (mtt) REVERT: C 6 ARG cc_start: 0.9405 (mtt90) cc_final: 0.8785 (mtt-85) REVERT: C 31 ARG cc_start: 0.9006 (mtt180) cc_final: 0.8770 (ttt180) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2551 time to fit residues: 19.5697 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 0.0570 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 overall best weight: 4.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 GLN ** 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 = 0.3345 r_free = 0.3345 target = 0.063444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048705 restraints weight = 40250.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050264 restraints weight = 23214.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051328 restraints weight = 15655.911| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4563 Z= 0.287 Angle : 0.768 6.142 6756 Z= 0.402 Chirality : 0.044 0.325 876 Planarity : 0.005 0.032 413 Dihedral : 27.561 175.007 2095 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 42.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.94 % Favored : 74.06 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -4.98 (0.51), residues: 212 helix: -3.18 (0.80), residues: 22 sheet: -3.24 (1.08), residues: 22 loop : -3.68 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS E 43 TYR 0.005 0.001 TYR E 48 ARG 0.005 0.001 ARG C 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.77 seconds wall clock time: 19 minutes 55.90 seconds (1195.90 seconds total)