Starting phenix.real_space_refine on Thu Dec 7 16:47:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/12_2023/6cu8_7619.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1780 2.51 5 N 510 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2880 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "C" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "G" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 288 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Time building chain proxies: 1.72, per 1000 atoms: 0.60 Number of scatterers: 2880 At special positions: 0 Unit cell: (96.3, 68.48, 44.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 590 8.00 N 510 7.00 C 1780 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: 0.98 Conformation dependent library (CDL) restraints added in 623.2 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.999A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.457A pdb=" N ALA E 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.939A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL D 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.567A pdb=" N THR B 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'F' and resid 81 through 82 removed outlier: 6.601A pdb=" N THR F 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 81 through 82 removed outlier: 6.633A pdb=" N THR G 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 13 hydrogen bonds defined for protein. 39 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 520 1.29 - 1.35: 452 1.35 - 1.42: 28 1.42 - 1.48: 480 1.48 - 1.55: 1400 Bond restraints: 2880 Sorted by residual: bond pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB ASN I 65 " pdb=" CG ASN I 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.15e+00 bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 2875 not shown) Histogram of bond angle deviations from ideal: 104.74 - 110.02: 625 110.02 - 115.30: 1475 115.30 - 120.58: 757 120.58 - 125.86: 1033 125.86 - 131.14: 10 Bond angle restraints: 3900 Sorted by residual: angle pdb=" C GLU G 57 " pdb=" N LYS G 58 " pdb=" CA LYS G 58 " ideal model delta sigma weight residual 122.19 124.91 -2.72 1.41e+00 5.03e-01 3.72e+00 angle pdb=" C GLY E 51 " pdb=" N VAL E 52 " pdb=" CA VAL E 52 " ideal model delta sigma weight residual 121.97 125.44 -3.47 1.80e+00 3.09e-01 3.72e+00 angle pdb=" C GLY C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta sigma weight residual 121.97 125.43 -3.46 1.80e+00 3.09e-01 3.70e+00 angle pdb=" C GLY I 51 " pdb=" N VAL I 52 " pdb=" CA VAL I 52 " ideal model delta sigma weight residual 121.97 125.42 -3.45 1.80e+00 3.09e-01 3.68e+00 angle pdb=" C GLU B 57 " pdb=" N LYS B 58 " pdb=" CA LYS B 58 " ideal model delta sigma weight residual 122.19 124.89 -2.70 1.41e+00 5.03e-01 3.67e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.30: 1190 4.30 - 8.59: 260 8.59 - 12.88: 141 12.88 - 17.18: 99 17.18 - 21.47: 30 Dihedral angle restraints: 1720 sinusoidal: 600 harmonic: 1120 Sorted by residual: dihedral pdb=" CA VAL C 74 " pdb=" C VAL C 74 " pdb=" N THR C 75 " pdb=" CA THR C 75 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL E 74 " pdb=" C VAL E 74 " pdb=" N THR E 75 " pdb=" CA THR E 75 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N THR B 75 " pdb=" CA THR B 75 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 317 0.033 - 0.066: 86 0.066 - 0.099: 44 0.099 - 0.132: 65 0.132 - 0.165: 28 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA VAL D 52 " pdb=" N VAL D 52 " pdb=" C VAL D 52 " pdb=" CB VAL D 52 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA VAL H 52 " pdb=" N VAL H 52 " pdb=" C VAL H 52 " pdb=" CB VAL H 52 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA VAL J 52 " pdb=" N VAL J 52 " pdb=" C VAL J 52 " pdb=" CB VAL J 52 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 537 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN G 79 " -0.004 2.00e-02 2.50e+03 7.48e-03 5.59e-01 pdb=" CD GLN G 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN G 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN G 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 79 " -0.004 2.00e-02 2.50e+03 7.43e-03 5.53e-01 pdb=" CD GLN A 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN A 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 79 " -0.004 2.00e-02 2.50e+03 7.41e-03 5.49e-01 pdb=" CD GLN E 79 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN E 79 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN E 79 " -0.004 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1138 2.91 - 3.41: 2277 3.41 - 3.90: 4694 3.90 - 4.40: 4410 4.40 - 4.90: 9453 Nonbonded interactions: 21972 Sorted by model distance: nonbonded pdb=" N ASN B 65 " pdb=" OD1 ASN B 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN J 65 " pdb=" OD1 ASN J 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN H 65 " pdb=" OD1 ASN H 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN C 65 " pdb=" OD1 ASN C 65 " model vdw 2.412 2.520 nonbonded pdb=" N ASN F 65 " pdb=" OD1 ASN F 65 " model vdw 2.412 2.520 ... (remaining 21967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.390 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: 1.680 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.220 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 0.027 2880 Z= 0.252 Angle : 0.726 3.470 3900 Z= 0.430 Chirality : 0.062 0.165 540 Planarity : 0.002 0.007 480 Dihedral : 7.746 21.472 1000 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -2.86 (0.47), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.36), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.332 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1215 time to fit residues: 16.5334 Evaluate side-chains 69 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 10 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN D 79 GLN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2880 Z= 0.240 Angle : 0.683 3.269 3900 Z= 0.408 Chirality : 0.054 0.119 540 Planarity : 0.003 0.013 480 Dihedral : 6.931 16.429 400 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.61 % Allowed : 13.87 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.344 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.0933 time to fit residues: 8.7743 Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0315 time to fit residues: 0.6158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 GLN B 79 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2880 Z= 0.244 Angle : 0.663 3.715 3900 Z= 0.394 Chirality : 0.055 0.120 540 Planarity : 0.003 0.014 480 Dihedral : 6.794 14.146 400 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.29 % Allowed : 17.10 % Favored : 81.61 % 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: -2.80 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.356 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 59 average time/residue: 0.0745 time to fit residues: 6.3214 Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0280 time to fit residues: 0.4548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2880 Z= 0.421 Angle : 0.786 5.007 3900 Z= 0.467 Chirality : 0.058 0.125 540 Planarity : 0.003 0.014 480 Dihedral : 7.676 19.252 400 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % Rotamer: Outliers : 3.23 % Allowed : 16.45 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.35), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.373 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.0906 time to fit residues: 6.1785 Evaluate side-chains 39 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0296 time to fit residues: 0.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2880 Z= 0.166 Angle : 0.571 3.497 3900 Z= 0.337 Chirality : 0.055 0.126 540 Planarity : 0.002 0.011 480 Dihedral : 6.383 14.589 400 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.29 % Allowed : 16.77 % Favored : 81.94 % 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: -2.85 (0.40), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.342 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.0798 time to fit residues: 6.1841 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0292 time to fit residues: 0.5011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2880 Z= 0.265 Angle : 0.641 5.306 3900 Z= 0.379 Chirality : 0.055 0.123 540 Planarity : 0.003 0.012 480 Dihedral : 6.672 23.101 400 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 3.55 % Allowed : 17.42 % Favored : 79.03 % 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: -3.00 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.317 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.1289 time to fit residues: 8.7247 Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0680 time to fit residues: 1.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2880 Z= 0.327 Angle : 0.686 4.588 3900 Z= 0.405 Chirality : 0.056 0.127 540 Planarity : 0.003 0.012 480 Dihedral : 7.152 26.381 400 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 1.94 % Allowed : 17.74 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.352 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1023 time to fit residues: 6.5275 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0302 time to fit residues: 0.5709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 2880 Z= 0.399 Angle : 0.738 4.615 3900 Z= 0.437 Chirality : 0.058 0.135 540 Planarity : 0.003 0.013 480 Dihedral : 7.615 26.096 400 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.49 % Favored : 80.51 % Rotamer: Outliers : 1.94 % Allowed : 18.71 % Favored : 79.35 % 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: -3.77 (0.35), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.342 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.0922 time to fit residues: 5.6958 Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0976 time to fit residues: 0.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2880 Z= 0.238 Angle : 0.615 5.024 3900 Z= 0.362 Chirality : 0.056 0.129 540 Planarity : 0.002 0.011 480 Dihedral : 6.792 22.729 400 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 20.32 % Favored : 79.68 % 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: -3.41 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0792 time to fit residues: 5.1189 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2880 Z= 0.289 Angle : 0.646 5.712 3900 Z= 0.381 Chirality : 0.056 0.126 540 Planarity : 0.003 0.012 480 Dihedral : 6.863 20.509 400 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.41 % Favored : 83.59 % Rotamer: Outliers : 0.32 % Allowed : 21.29 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.362 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0799 time to fit residues: 5.0824 Evaluate side-chains 44 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0343 time to fit residues: 0.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 overall best weight: 3.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.119429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.105566 restraints weight = 7098.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.107978 restraints weight = 3580.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.109543 restraints weight = 2255.603| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2880 Z= 0.183 Angle : 0.571 5.053 3900 Z= 0.335 Chirality : 0.054 0.125 540 Planarity : 0.002 0.011 480 Dihedral : 6.264 18.669 400 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.65 % Allowed : 20.97 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS H 50 =============================================================================== Job complete usr+sys time: 819.91 seconds wall clock time: 15 minutes 51.27 seconds (951.27 seconds total)