Starting phenix.real_space_refine on Fri Dec 8 16:26:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5w_33627/12_2023/7y5w_33627.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 202 5.49 5 S 20 5.16 5 C 4911 2.51 5 N 1652 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "E" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 591 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "H" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 524 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2054 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "J" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2087 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Time building chain proxies: 4.86, per 1000 atoms: 0.55 Number of scatterers: 8811 At special positions: 0 Unit cell: (82, 114, 116, 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 20 16.00 P 202 15.00 O 2026 8.00 N 1652 7.00 C 4911 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: 4.70 Conformation dependent library (CDL) restraints added in 969.7 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 79.1% alpha, 1.7% beta 90 base pairs and 167 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.653A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.501A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 76 removed outlier: 4.209A pdb=" N TYR D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.503A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.803A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.247A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.326A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 231 hydrogen bonds 442 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 167 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1879 1.34 - 1.45: 2816 1.45 - 1.57: 4233 1.57 - 1.69: 402 1.69 - 1.81: 32 Bond restraints: 9362 Sorted by residual: bond pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" C3' DG J 84 " pdb=" O3' DG J 84 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CG1 ILE G 112 " pdb=" CD1 ILE G 112 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CB GLU G 105 " pdb=" CG GLU G 105 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.35e-01 bond pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.07e-01 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 98.09 - 104.97: 817 104.97 - 111.86: 5110 111.86 - 118.74: 2425 118.74 - 125.63: 4469 125.63 - 132.51: 667 Bond angle restraints: 13488 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 121.72 -9.02 3.00e+00 1.11e-01 9.05e+00 angle pdb=" C3' DG I 121 " pdb=" C2' DG I 121 " pdb=" C1' DG I 121 " ideal model delta sigma weight residual 101.60 98.09 3.51 1.50e+00 4.44e-01 5.48e+00 angle pdb=" CB GLU G 105 " pdb=" CG GLU G 105 " pdb=" CD GLU G 105 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.70e+00 3.46e-01 5.16e+00 angle pdb=" CB ARG B 40 " pdb=" CG ARG B 40 " pdb=" CD ARG B 40 " ideal model delta sigma weight residual 111.30 116.14 -4.84 2.30e+00 1.89e-01 4.42e+00 angle pdb=" C2' DG I 121 " pdb=" C1' DG I 121 " pdb=" N9 DG I 121 " ideal model delta sigma weight residual 113.50 116.46 -2.96 1.50e+00 4.44e-01 3.90e+00 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 3940 29.06 - 58.13: 1086 58.13 - 87.19: 104 87.19 - 116.25: 1 116.25 - 145.31: 4 Dihedral angle restraints: 5135 sinusoidal: 3448 harmonic: 1687 Sorted by residual: dihedral pdb=" C4' DG I 73 " pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " pdb=" P DC I 74 " ideal model delta sinusoidal sigma weight residual 220.00 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DT J 105 " pdb=" C3' DT J 105 " pdb=" O3' DT J 105 " pdb=" P DG J 106 " ideal model delta sinusoidal sigma weight residual 220.00 89.58 130.42 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual 220.00 91.20 128.80 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1110 0.029 - 0.059: 327 0.059 - 0.088: 77 0.088 - 0.118: 29 0.118 - 0.147: 6 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA ILE D 29 " pdb=" N ILE D 29 " pdb=" C ILE D 29 " pdb=" CB ILE D 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE D 46 " pdb=" N ILE D 46 " pdb=" C ILE D 46 " pdb=" CB ILE D 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1546 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 121 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.023 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 121 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 110 " -0.020 2.00e-02 2.50e+03 9.51e-03 2.04e+00 pdb=" N1 DC I 110 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC I 110 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 110 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 110 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 110 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 110 " 0.004 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 7704 3.22 - 3.78: 17065 3.78 - 4.34: 20536 4.34 - 4.90: 29648 Nonbonded interactions: 75172 Sorted by model distance: nonbonded pdb=" N2 DG I 34 " pdb=" O2 DC J 114 " model vdw 2.102 2.496 nonbonded pdb=" N2 DG I 33 " pdb=" O2 DC J 115 " model vdw 2.118 2.496 nonbonded pdb=" N2 DG I 85 " pdb=" O2 DC J 63 " model vdw 2.139 2.496 nonbonded pdb=" O2 DC I 82 " pdb=" N2 DG J 66 " model vdw 2.156 2.496 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.228 2.440 ... (remaining 75167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 61 through 133) selection = (chain 'C' and resid 61 through 133) selection = (chain 'E' and resid 61 through 133) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 29 through 93) selection = (chain 'D' and resid 29 through 93) selection = (chain 'F' and resid 29 through 93) selection = chain 'H' } 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: 1.140 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: 3.870 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.700 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.003 0.040 9362 Z= 0.185 Angle : 0.533 9.023 13488 Z= 0.314 Chirality : 0.032 0.147 1549 Planarity : 0.003 0.045 1004 Dihedral : 27.557 145.314 4035 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 2.53 (0.34), residues: 563 helix: 2.20 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 113 PHE 0.007 0.001 PHE E 67 TYR 0.008 0.001 TYR B 51 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 0.753 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3010 time to fit residues: 120.4225 Evaluate side-chains 222 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN B 93 GLN C 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9362 Z= 0.231 Angle : 0.666 11.873 13488 Z= 0.371 Chirality : 0.037 0.245 1549 Planarity : 0.005 0.046 1004 Dihedral : 30.628 146.604 2840 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.25 % Allowed : 26.72 % Favored : 69.03 % 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: 2.18 (0.34), residues: 563 helix: 1.91 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.74 (0.51), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.022 0.002 PHE G 67 TYR 0.018 0.002 TYR H 88 ARG 0.009 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 0.758 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 outliers start: 21 outliers final: 12 residues processed: 265 average time/residue: 0.2817 time to fit residues: 94.5621 Evaluate side-chains 242 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1056 time to fit residues: 2.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 overall best weight: 2.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9362 Z= 0.295 Angle : 0.687 10.410 13488 Z= 0.389 Chirality : 0.037 0.170 1549 Planarity : 0.005 0.041 1004 Dihedral : 30.849 150.682 2840 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.85 % Allowed : 30.77 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.34), residues: 563 helix: 1.64 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.75 (0.53), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.022 0.003 PHE H 61 TYR 0.011 0.002 TYR F 88 ARG 0.010 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 237 time to evaluate : 0.745 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: symmetry clash outliers start: 19 outliers final: 10 residues processed: 243 average time/residue: 0.2806 time to fit residues: 85.7931 Evaluate side-chains 228 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 218 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0812 time to fit residues: 2.3172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9362 Z= 0.270 Angle : 0.692 11.208 13488 Z= 0.389 Chirality : 0.037 0.164 1549 Planarity : 0.004 0.038 1004 Dihedral : 30.897 153.069 2840 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.64 % Allowed : 31.38 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.34), residues: 563 helix: 1.56 (0.24), residues: 466 sheet: None (None), residues: 0 loop : -0.83 (0.53), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 113 PHE 0.013 0.002 PHE H 61 TYR 0.017 0.001 TYR H 88 ARG 0.006 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 0.720 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 outliers start: 18 outliers final: 10 residues processed: 245 average time/residue: 0.3055 time to fit residues: 94.1973 Evaluate side-chains 230 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1308 time to fit residues: 2.8050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9362 Z= 0.247 Angle : 0.700 11.435 13488 Z= 0.388 Chirality : 0.036 0.156 1549 Planarity : 0.005 0.093 1004 Dihedral : 30.881 154.261 2840 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.83 % Allowed : 35.63 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.34), residues: 563 helix: 1.52 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.029 0.002 PHE G 78 TYR 0.016 0.001 TYR H 88 ARG 0.014 0.001 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 0.722 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 outliers start: 14 outliers final: 9 residues processed: 246 average time/residue: 0.2844 time to fit residues: 88.4105 Evaluate side-chains 229 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 220 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1344 time to fit residues: 2.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9362 Z= 0.271 Angle : 0.738 11.199 13488 Z= 0.405 Chirality : 0.037 0.161 1549 Planarity : 0.004 0.039 1004 Dihedral : 30.891 155.006 2840 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.44 % Allowed : 37.04 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.34), residues: 563 helix: 1.34 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.19 (0.51), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.029 0.002 PHE G 78 TYR 0.018 0.001 TYR H 88 ARG 0.008 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 0.759 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 outliers start: 17 outliers final: 15 residues processed: 232 average time/residue: 0.2847 time to fit residues: 82.9443 Evaluate side-chains 225 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0839 time to fit residues: 3.0610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9362 Z= 0.314 Angle : 0.762 10.698 13488 Z= 0.422 Chirality : 0.038 0.161 1549 Planarity : 0.005 0.047 1004 Dihedral : 30.996 155.543 2840 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.02 % Allowed : 37.85 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.34), residues: 563 helix: 1.25 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.15 (0.50), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 113 PHE 0.040 0.002 PHE G 78 TYR 0.019 0.002 TYR H 88 ARG 0.015 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 223 time to evaluate : 0.755 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: symmetry clash outliers start: 10 outliers final: 9 residues processed: 226 average time/residue: 0.2907 time to fit residues: 82.5712 Evaluate side-chains 216 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 207 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1400 time to fit residues: 2.8520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9362 Z= 0.345 Angle : 0.816 15.253 13488 Z= 0.446 Chirality : 0.040 0.191 1549 Planarity : 0.006 0.107 1004 Dihedral : 31.148 156.176 2840 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.23 % Allowed : 37.65 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.34), residues: 563 helix: 1.12 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.28 (0.50), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 113 PHE 0.031 0.002 PHE G 78 TYR 0.019 0.002 TYR H 88 ARG 0.017 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 0.786 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 outliers start: 11 outliers final: 6 residues processed: 221 average time/residue: 0.2959 time to fit residues: 81.9517 Evaluate side-chains 213 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 207 time to evaluate : 0.737 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0876 time to fit residues: 1.8233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 9362 Z= 0.436 Angle : 0.891 14.013 13488 Z= 0.488 Chirality : 0.043 0.202 1549 Planarity : 0.006 0.078 1004 Dihedral : 31.492 156.989 2840 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.23 % Allowed : 39.68 % Favored : 58.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.33), residues: 563 helix: 0.84 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 113 PHE 0.025 0.003 PHE G 78 TYR 0.014 0.002 TYR F 72 ARG 0.016 0.001 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 208 average time/residue: 0.2875 time to fit residues: 75.0320 Evaluate side-chains 201 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0847 time to fit residues: 1.6905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9362 Z= 0.318 Angle : 0.889 14.941 13488 Z= 0.476 Chirality : 0.041 0.289 1549 Planarity : 0.006 0.065 1004 Dihedral : 31.401 156.707 2840 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 42.91 % Favored : 56.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.33), residues: 563 helix: 0.90 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -1.21 (0.49), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 113 PHE 0.023 0.002 PHE G 78 TYR 0.018 0.002 TYR H 72 ARG 0.015 0.001 ARG H 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 0.672 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: symmetry clash outliers start: 5 outliers final: 3 residues processed: 215 average time/residue: 0.2838 time to fit residues: 76.4183 Evaluate side-chains 209 residues out of total 494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0860 time to fit residues: 1.2088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 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 = 0.3538 r_free = 0.3538 target = 0.055441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.039609 restraints weight = 57172.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040873 restraints weight = 28523.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.041622 restraints weight = 18990.101| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9362 Z= 0.268 Angle : 0.876 15.146 13488 Z= 0.464 Chirality : 0.040 0.271 1549 Planarity : 0.006 0.059 1004 Dihedral : 31.181 156.964 2840 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 43.32 % Favored : 56.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.34), residues: 563 helix: 0.89 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.26 (0.50), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 113 PHE 0.026 0.002 PHE G 67 TYR 0.018 0.002 TYR H 72 ARG 0.013 0.001 ARG D 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.92 seconds wall clock time: 38 minutes 1.03 seconds (2281.03 seconds total)