Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:00:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/11_2022/6cu8_7619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/11_2022/6cu8_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_7619/11_2022/6cu8_7619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/11_2022/6cu8_7619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/11_2022/6cu8_7619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cu8_7619/11_2022/6cu8_7619.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 1.76, per 1000 atoms: 0.61 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: 1.01 Conformation dependent library (CDL) restraints added in 437.2 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: 0.18 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: 0.60 Time building geometry restraints manager: 1.10 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 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. 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: 0.370 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: 1.730 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 % 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 *********************** 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 : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1180 time to fit residues: 16.3962 Evaluate side-chains 69 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4534 ------------------------------------------------------------------------------- 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: 8.9990 chunk 12 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3232 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= 0.233 Angle : 0.678 3.328 3900 Z= 0.405 Chirality : 0.054 0.119 540 Planarity : 0.003 0.013 480 Dihedral : 6.912 16.084 400 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 1.61 % 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: -2.70 (0.44), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 390 *********************** 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 71 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.344 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.0836 time to fit residues: 7.8857 Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0286 time to fit residues: 0.6014 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN C 79 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 2880 Z= 0.333 Angle : 0.743 4.376 3900 Z= 0.443 Chirality : 0.056 0.127 540 Planarity : 0.003 0.014 480 Dihedral : 7.384 16.833 400 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer Outliers : 1.29 % 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: -3.29 (0.38), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.29), residues: 390 *********************** 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 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.0925 time to fit residues: 6.7200 Evaluate side-chains 41 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0305 time to fit residues: 0.5670 ------------------------------------------------------------------------------- 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: 30.0000 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 7.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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: 0.7467 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2880 Z= 0.298 Angle : 0.676 3.680 3900 Z= 0.402 Chirality : 0.056 0.124 540 Planarity : 0.003 0.013 480 Dihedral : 7.074 16.664 400 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer Outliers : 2.58 % 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 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.28), residues: 390 *********************** 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 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.314 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.0789 time to fit residues: 5.6415 Evaluate side-chains 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0304 time to fit residues: 0.7251 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 2880 Z= 0.189 Angle : 0.582 3.504 3900 Z= 0.344 Chirality : 0.054 0.125 540 Planarity : 0.002 0.012 480 Dihedral : 6.372 17.854 400 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 1.61 % 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: -2.70 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 390 *********************** 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 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.531 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 0.0844 time to fit residues: 6.3942 Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0262 time to fit residues: 0.4861 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 0.0040 chunk 32 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 overall best weight: 5.4002 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2880 Z= 0.233 Angle : 0.605 3.513 3900 Z= 0.359 Chirality : 0.055 0.121 540 Planarity : 0.002 0.012 480 Dihedral : 6.460 23.828 400 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.31), residues: 390 *********************** 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 59 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.375 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.1046 time to fit residues: 8.0679 Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0300 time to fit residues: 0.7330 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.7467 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2880 Z= 0.297 Angle : 0.652 3.570 3900 Z= 0.387 Chirality : 0.056 0.123 540 Planarity : 0.003 0.013 480 Dihedral : 6.829 20.752 400 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.29), residues: 390 *********************** 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 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.336 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 0.1053 time to fit residues: 7.2541 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1204 time to fit residues: 1.3432 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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: 0.7379 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 2880 Z= 0.182 Angle : 0.561 4.670 3900 Z= 0.331 Chirality : 0.054 0.125 540 Planarity : 0.002 0.012 480 Dihedral : 6.141 21.483 400 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.97 % 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: -2.71 (0.41), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 390 *********************** 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 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.275 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0788 time to fit residues: 5.5184 Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0294 time to fit residues: 0.5791 ------------------------------------------------------------------------------- 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: 20.0000 chunk 23 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 overall best weight: 6.4790 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.5916 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= 0.270 Angle : 0.622 5.674 3900 Z= 0.367 Chirality : 0.055 0.124 540 Planarity : 0.002 0.011 480 Dihedral : 6.480 18.587 400 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 390 *********************** 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 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.348 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.0803 time to fit residues: 4.8244 Evaluate side-chains 38 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4611 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.0270 chunk 27 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- 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: 0.7416 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2880 Z= 0.224 Angle : 0.586 4.983 3900 Z= 0.345 Chirality : 0.054 0.123 540 Planarity : 0.002 0.011 480 Dihedral : 6.283 19.008 400 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.39), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.30), residues: 390 ********************** 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 42 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0692 time to fit residues: 4.4034 Evaluate side-chains 40 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4587 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.117100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.103254 restraints weight = 7187.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.105556 restraints weight = 3681.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.107099 restraints weight = 2348.731| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2880 Z= 0.305 Angle : 0.649 5.872 3900 Z= 0.383 Chirality : 0.055 0.129 540 Planarity : 0.003 0.012 480 Dihedral : 6.711 17.337 400 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.90 % Favored : 84.10 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.37), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 390 =============================================================================== Job complete usr+sys time: 773.69 seconds wall clock time: 14 minutes 54.15 seconds (894.15 seconds total)