Starting phenix.real_space_refine on Mon Sep 23 18:18:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/09_2024/7yr6_34047.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/09_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_34047/09_2024/7yr6_34047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/09_2024/7yr6_34047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/09_2024/7yr6_34047.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr6_34047/09_2024/7yr6_34047.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.38, per 1000 atoms: 0.80 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 - 3.00 Amino acid : True - 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: 1.05 Conformation dependent library (CDL) restraints added in 224.2 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: 1.58 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: 1.05 Time building geometry restraints manager: 1.24 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: 0.00 - 2.00: 6451 2.00 - 4.01: 267 4.01 - 6.01: 29 6.01 - 8.01: 6 8.01 - 10.01: 3 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 3.040 nonbonded pdb=" O2' A A 41 " pdb=" O5' G A 43 " model vdw 2.326 3.040 nonbonded pdb=" O GLU B 10 " pdb=" OG1 THR B 21 " model vdw 2.342 3.040 nonbonded pdb=" O VAL E 40 " pdb=" N1 G A 10 " model vdw 2.370 3.120 nonbonded pdb=" O VAL B 42 " pdb=" N2 G A 39 " model vdw 2.397 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.770 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.100 Find NCS groups from input model: 0.090 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- 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 : 0.293 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: 0.2502 time to fit residues: 24.2536 Evaluate side-chains 59 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4563 Z= 0.165 Angle : 0.591 5.392 6756 Z= 0.314 Chirality : 0.037 0.163 876 Planarity : 0.004 0.023 413 Dihedral : 26.617 171.457 2095 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 0.55 % Allowed : 7.14 % Favored : 92.31 % 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: -5.11 (0.47), residues: 212 helix: -2.71 (0.86), residues: 28 sheet: -2.85 (1.08), residues: 22 loop : -3.96 (0.39), 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 0.007 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 64 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.305 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 13 MET cc_start: 0.9411 (tmm) cc_final: 0.9035 (tmm) REVERT: C 4 LEU cc_start: 0.9483 (mm) cc_final: 0.9252 (mm) REVERT: C 31 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8776 (ttt180) REVERT: B 1 MET cc_start: 0.6665 (mpp) cc_final: 0.6421 (mpp) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2416 time to fit residues: 17.7609 Evaluate side-chains 53 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 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: 8.9990 chunk 22 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 35 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4563 Z= 0.387 Angle : 0.869 7.877 6756 Z= 0.447 Chirality : 0.047 0.238 876 Planarity : 0.007 0.056 413 Dihedral : 27.544 171.338 2095 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 39.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.53 % Favored : 75.47 % Rotamer: Outliers : 1.65 % Allowed : 13.19 % Favored : 85.16 % 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: -5.68 (0.46), residues: 212 helix: -3.14 (0.74), residues: 28 sheet: -3.19 (1.00), residues: 22 loop : -4.39 (0.40), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS B 43 TYR 0.004 0.001 TYR E 48 ARG 0.009 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 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 MET cc_start: 0.9465 (tmm) cc_final: 0.9199 (tmm) REVERT: E 44 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7885 (mtt180) REVERT: E 47 ILE cc_start: 0.7857 (mp) cc_final: 0.7553 (mp) REVERT: C 2 LEU cc_start: 0.8251 (mm) cc_final: 0.8022 (mm) REVERT: B 1 MET cc_start: 0.7712 (mpp) cc_final: 0.7223 (mpp) outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.2507 time to fit residues: 16.7123 Evaluate side-chains 46 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4563 Z= 0.306 Angle : 0.767 7.544 6756 Z= 0.397 Chirality : 0.044 0.267 876 Planarity : 0.005 0.030 413 Dihedral : 27.516 167.267 2095 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.23 % Favored : 78.77 % Rotamer: Outliers : 0.55 % Allowed : 12.64 % Favored : 86.81 % 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: -5.57 (0.48), residues: 212 helix: -3.25 (0.67), residues: 28 sheet: -3.30 (0.98), residues: 22 loop : -4.24 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS B 43 TYR 0.004 0.001 TYR C 48 ARG 0.005 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 56 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8864 (ttp) cc_final: 0.8097 (tmm) REVERT: E 2 LEU cc_start: 0.9613 (tp) cc_final: 0.9336 (tp) REVERT: E 13 MET cc_start: 0.9499 (tmm) cc_final: 0.9246 (tmm) REVERT: E 44 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7696 (mtt180) REVERT: E 47 ILE cc_start: 0.8055 (mp) cc_final: 0.7841 (mp) REVERT: C 2 LEU cc_start: 0.8075 (mm) cc_final: 0.7867 (mm) REVERT: B 1 MET cc_start: 0.7327 (mpp) cc_final: 0.6779 (mpp) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2550 time to fit residues: 16.3002 Evaluate side-chains 43 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.0980 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 43 HIS ** 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: 0.7736 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4563 Z= 0.348 Angle : 0.824 8.607 6756 Z= 0.426 Chirality : 0.046 0.291 876 Planarity : 0.006 0.047 413 Dihedral : 27.744 168.267 2095 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 37.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Rotamer: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.68 (0.47), residues: 212 helix: -3.00 (0.70), residues: 28 sheet: -3.05 (1.06), residues: 22 loop : -4.44 (0.41), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS B 43 TYR 0.017 0.002 TYR B 48 ARG 0.007 0.001 ARG C 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 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.391 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: E 1 MET cc_start: 0.9018 (ttp) cc_final: 0.8279 (tmm) REVERT: E 2 LEU cc_start: 0.9623 (tp) cc_final: 0.9348 (tp) REVERT: E 13 MET cc_start: 0.9544 (tmm) cc_final: 0.9268 (tmm) REVERT: E 47 ILE cc_start: 0.8042 (mp) cc_final: 0.7840 (mp) REVERT: D 48 TYR cc_start: 0.9190 (t80) cc_final: 0.8986 (t80) REVERT: C 2 LEU cc_start: 0.8103 (mm) cc_final: 0.7852 (mm) REVERT: B 1 MET cc_start: 0.7515 (mpp) cc_final: 0.7199 (mpp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2633 time to fit residues: 17.0618 Evaluate side-chains 42 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 HIS E 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4563 Z= 0.179 Angle : 0.658 7.279 6756 Z= 0.346 Chirality : 0.040 0.210 876 Planarity : 0.004 0.019 413 Dihedral : 27.239 166.249 2095 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.45 % Favored : 82.55 % 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: -5.32 (0.50), residues: 212 helix: -3.61 (0.59), residues: 28 sheet: -2.56 (1.15), residues: 22 loop : -4.03 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 43 TYR 0.006 0.001 TYR E 48 ARG 0.005 0.001 ARG E 44 *********************** 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 62 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.259 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: E 1 MET cc_start: 0.8857 (ttp) cc_final: 0.8083 (tmm) REVERT: E 2 LEU cc_start: 0.9636 (tp) cc_final: 0.9310 (tp) REVERT: E 13 MET cc_start: 0.9517 (tmm) cc_final: 0.9188 (tmm) REVERT: E 44 ARG cc_start: 0.6412 (ptp-170) cc_final: 0.5989 (mtt180) REVERT: D 13 MET cc_start: 0.7225 (tmm) cc_final: 0.6914 (tmm) REVERT: C 1 MET cc_start: 0.3622 (mtt) cc_final: 0.2478 (mtt) REVERT: B 1 MET cc_start: 0.6870 (mpp) cc_final: 0.6496 (mpp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2434 time to fit residues: 17.4204 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 0.0000 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4563 Z= 0.147 Angle : 0.615 6.725 6756 Z= 0.321 Chirality : 0.038 0.202 876 Planarity : 0.004 0.018 413 Dihedral : 26.876 166.268 2095 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % 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: -5.11 (0.51), residues: 212 helix: -3.48 (0.67), residues: 28 sheet: -2.50 (1.10), residues: 22 loop : -3.86 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 43 TYR 0.003 0.001 TYR E 48 ARG 0.004 0.001 ARG B 7 *********************** 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 65 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.254 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: 0.8766 (ttp) cc_final: 0.8220 (tmm) REVERT: E 13 MET cc_start: 0.9442 (tmm) cc_final: 0.9087 (tmm) REVERT: D 48 TYR cc_start: 0.9325 (t80) cc_final: 0.9121 (t80) REVERT: C 1 MET cc_start: 0.3414 (mtt) cc_final: 0.2326 (mtt) REVERT: B 1 MET cc_start: 0.6931 (mpp) cc_final: 0.6607 (mpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2483 time to fit residues: 18.6191 Evaluate side-chains 49 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 0.0070 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4563 Z= 0.285 Angle : 0.741 6.131 6756 Z= 0.386 Chirality : 0.043 0.248 876 Planarity : 0.005 0.029 413 Dihedral : 27.308 167.339 2095 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 31.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.11 % Favored : 76.89 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -5.12 (0.53), residues: 212 helix: -3.41 (0.70), residues: 28 sheet: -2.68 (1.47), residues: 12 loop : -3.84 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 43 TYR 0.004 0.001 TYR B 48 ARG 0.005 0.001 ARG C 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 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.278 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: 0.8954 (ttp) cc_final: 0.8209 (tmm) REVERT: E 2 LEU cc_start: 0.9622 (tp) cc_final: 0.9338 (tp) REVERT: E 13 MET cc_start: 0.9521 (tmm) cc_final: 0.9241 (tmm) REVERT: C 31 ARG cc_start: 0.9081 (mtt180) cc_final: 0.8849 (ttt180) REVERT: B 1 MET cc_start: 0.7441 (mpp) cc_final: 0.7133 (mpp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2437 time to fit residues: 15.6073 Evaluate side-chains 47 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 6.9990 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: 6.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5713 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= 0.378 Angle : 0.869 10.139 6756 Z= 0.452 Chirality : 0.048 0.291 876 Planarity : 0.006 0.057 413 Dihedral : 27.667 167.945 2095 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 39.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -5.57 (0.48), residues: 212 helix: -3.57 (0.64), residues: 28 sheet: -2.88 (1.34), residues: 12 loop : -4.21 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS B 43 TYR 0.008 0.002 TYR D 48 ARG 0.008 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 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.9080 (ttp) cc_final: 0.8705 (tmm) REVERT: E 13 MET cc_start: 0.9558 (tmm) cc_final: 0.9243 (tmm) REVERT: E 47 ILE cc_start: 0.8453 (mp) cc_final: 0.8051 (mp) REVERT: E 50 ARG cc_start: 0.9486 (pmt170) cc_final: 0.9242 (pmt170) REVERT: D 1 MET cc_start: 0.4296 (tpt) cc_final: 0.4003 (tpt) REVERT: D 13 MET cc_start: 0.7985 (tmm) cc_final: 0.7614 (tmm) REVERT: B 1 MET cc_start: 0.7449 (mpp) cc_final: 0.7124 (mpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2530 time to fit residues: 15.2736 Evaluate side-chains 42 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 0.3980 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4563 Z= 0.178 Angle : 0.675 9.286 6756 Z= 0.351 Chirality : 0.040 0.267 876 Planarity : 0.004 0.029 413 Dihedral : 27.017 165.658 2095 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.34 % Favored : 80.66 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -5.30 (0.50), residues: 212 helix: -3.60 (0.60), residues: 28 sheet: -2.83 (1.43), residues: 12 loop : -3.95 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 43 TYR 0.011 0.001 TYR C 48 ARG 0.005 0.001 ARG C 44 ********************** 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 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.298 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: 0.8785 (ttp) cc_final: 0.8339 (tmm) REVERT: E 13 MET cc_start: 0.9534 (tmm) cc_final: 0.9222 (tmm) REVERT: C 1 MET cc_start: 0.3715 (mtt) cc_final: 0.2634 (mtt) REVERT: B 1 MET cc_start: 0.6745 (mpp) cc_final: 0.6358 (mpp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2680 time to fit residues: 18.0412 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: 6.9990 chunk 28 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.065445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050945 restraints weight = 40497.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052469 restraints weight = 23803.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053505 restraints weight = 16205.668| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5602 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= 0.268 Angle : 0.745 9.200 6756 Z= 0.389 Chirality : 0.043 0.310 876 Planarity : 0.005 0.035 413 Dihedral : 27.226 167.707 2095 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -5.36 (0.50), residues: 212 helix: -3.68 (0.65), residues: 28 sheet: -2.92 (1.41), residues: 12 loop : -3.99 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 43 TYR 0.010 0.001 TYR C 48 ARG 0.012 0.001 ARG E 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.70 seconds wall clock time: 19 minutes 47.94 seconds (1187.94 seconds total)