Starting phenix.real_space_refine on Mon Sep 23 23:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk9_19265/09_2024/8rk9_19265.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 3912 2.51 5 N 1074 2.21 5 O 1152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6138 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1023 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 4.51, per 1000 atoms: 0.73 Number of scatterers: 6138 At special positions: 0 Unit cell: (95.864, 95.864, 57.5184, 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 1152 8.00 N 1074 7.00 C 3912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 822.1 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 12 sheets defined 19.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA A 68 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 69 " --> pdb=" O GLN A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 5.027A pdb=" N ARG B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA B 68 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 69 " --> pdb=" O GLN B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 69' Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA C 68 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 69 " --> pdb=" O GLN C 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 69' Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA D 68 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 69 " --> pdb=" O GLN D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA E 68 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE E 69 " --> pdb=" O GLN E 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 69' Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 removed outlier: 5.028A pdb=" N ARG F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 69 removed outlier: 3.754A pdb=" N ALA F 68 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE F 69 " --> pdb=" O GLN F 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 69' Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.881A pdb=" N LEU F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=2, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=3, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=5, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=6, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=7, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=8, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=9, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=10, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=11, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=12, first strand: chain 'F' and resid 49 through 50 120 hydrogen bonds defined for protein. 324 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: 1.29 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1014 1.29 - 1.36: 1056 1.36 - 1.42: 588 1.42 - 1.48: 984 1.48 - 1.55: 2640 Bond restraints: 6282 Sorted by residual: bond pdb=" CA VAL A 22 " pdb=" CB VAL A 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.72e-01 bond pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.72e-01 bond pdb=" CA VAL E 22 " pdb=" CB VAL E 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.56e-01 bond pdb=" CA VAL B 22 " pdb=" CB VAL B 22 " ideal model delta sigma weight residual 1.537 1.540 -0.003 5.00e-03 4.00e+04 4.56e-01 bond pdb=" CA ARG F 67 " pdb=" CB ARG F 67 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.69e-02 3.50e+03 4.53e-01 ... (remaining 6277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 8356 1.76 - 3.53: 188 3.53 - 5.29: 24 5.29 - 7.06: 0 7.06 - 8.82: 12 Bond angle restraints: 8580 Sorted by residual: angle pdb=" C GLN C 66 " pdb=" N ARG C 67 " pdb=" CA ARG C 67 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.19e+00 angle pdb=" C GLN E 66 " pdb=" N ARG E 67 " pdb=" CA ARG E 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C GLN B 66 " pdb=" N ARG B 67 " pdb=" CA ARG B 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C GLN A 66 " pdb=" N ARG A 67 " pdb=" CA ARG A 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 angle pdb=" C GLN D 66 " pdb=" N ARG D 67 " pdb=" CA ARG D 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.15e+00 ... (remaining 8575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 3343 16.74 - 33.49: 245 33.49 - 50.23: 72 50.23 - 66.97: 18 66.97 - 83.72: 18 Dihedral angle restraints: 3696 sinusoidal: 1392 harmonic: 2304 Sorted by residual: dihedral pdb=" CA ARG D 123 " pdb=" CB ARG D 123 " pdb=" CG ARG D 123 " pdb=" CD ARG D 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.55 44.55 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG A 123 " pdb=" CB ARG A 123 " pdb=" CG ARG A 123 " pdb=" CD ARG A 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.55 44.55 3 1.50e+01 4.44e-03 8.01e+00 dihedral pdb=" CA ARG B 123 " pdb=" CB ARG B 123 " pdb=" CG ARG B 123 " pdb=" CD ARG B 123 " ideal model delta sinusoidal sigma weight residual -60.00 -104.53 44.53 3 1.50e+01 4.44e-03 8.01e+00 ... (remaining 3693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 504 0.025 - 0.050: 242 0.050 - 0.075: 95 0.075 - 0.100: 63 0.100 - 0.125: 62 Chirality restraints: 966 Sorted by residual: chirality pdb=" CA ILE E 69 " pdb=" N ILE E 69 " pdb=" C ILE E 69 " pdb=" CB ILE E 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 963 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 66 " -0.005 2.00e-02 2.50e+03 9.17e-03 8.41e-01 pdb=" C GLN F 66 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN F 66 " -0.006 2.00e-02 2.50e+03 pdb=" N ARG F 67 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 66 " 0.005 2.00e-02 2.50e+03 9.11e-03 8.31e-01 pdb=" C GLN D 66 " -0.016 2.00e-02 2.50e+03 pdb=" O GLN D 66 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG D 67 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 66 " -0.005 2.00e-02 2.50e+03 9.11e-03 8.31e-01 pdb=" C GLN A 66 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN A 66 " -0.006 2.00e-02 2.50e+03 pdb=" N ARG A 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1868 2.81 - 3.34: 5941 3.34 - 3.86: 9577 3.86 - 4.38: 10559 4.38 - 4.90: 17722 Nonbonded interactions: 45667 Sorted by model distance: nonbonded pdb=" OH TYR B 51 " pdb=" OE1 GLN B 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR C 51 " pdb=" OE1 GLN C 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 51 " pdb=" OE1 GLN A 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR D 51 " pdb=" OE1 GLN D 74 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR E 51 " pdb=" OE1 GLN E 74 " model vdw 2.294 3.040 ... (remaining 45662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 7.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.230 Find NCS groups from input model: 0.370 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0031 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 : 0.002 0.017 6282 Z= 0.145 Angle : 0.670 8.821 8580 Z= 0.324 Chirality : 0.046 0.125 966 Planarity : 0.003 0.016 1128 Dihedral : 15.379 83.718 2232 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.28), residues: 792 helix: -1.04 (0.59), residues: 96 sheet: -2.07 (0.42), residues: 156 loop : -3.16 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 76 HIS 0.001 0.000 HIS C 62 PHE 0.004 0.001 PHE C 9 TYR 0.007 0.001 TYR B 138 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2694 time to fit residues: 33.8954 Evaluate side-chains 34 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 62 HIS D 62 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS F 62 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0361 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6282 Z= 0.243 Angle : 0.826 8.273 8580 Z= 0.395 Chirality : 0.052 0.128 966 Planarity : 0.008 0.063 1128 Dihedral : 4.432 14.429 894 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 1.28 % Allowed : 11.38 % Favored : 87.34 % 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: -3.84 (0.27), residues: 792 helix: -1.17 (0.55), residues: 96 sheet: -1.89 (0.43), residues: 144 loop : -3.24 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 76 HIS 0.002 0.001 HIS D 62 PHE 0.018 0.002 PHE F 147 TYR 0.013 0.001 TYR D 51 ARG 0.008 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.2210 time to fit residues: 9.1241 Evaluate side-chains 20 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain F residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.0010 chunk 63 optimal weight: 0.0020 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 53 optimal weight: 0.0070 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0267 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6282 Z= 0.175 Angle : 0.690 8.350 8580 Z= 0.325 Chirality : 0.048 0.117 966 Planarity : 0.006 0.043 1128 Dihedral : 4.017 12.058 894 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.85 % Allowed : 13.94 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.28), residues: 792 helix: -1.40 (0.54), residues: 102 sheet: -1.80 (0.42), residues: 144 loop : -3.15 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 76 HIS 0.001 0.000 HIS D 62 PHE 0.014 0.001 PHE F 147 TYR 0.005 0.001 TYR B 51 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 26 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 50 average time/residue: 0.1202 time to fit residues: 9.7041 Evaluate side-chains 24 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 16 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 0.0030 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.0020 chunk 42 optimal weight: 0.0170 overall best weight: 0.0232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0281 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6282 Z= 0.175 Angle : 0.684 8.029 8580 Z= 0.326 Chirality : 0.047 0.117 966 Planarity : 0.006 0.037 1128 Dihedral : 3.962 11.404 894 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.53 % Allowed : 16.03 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.27), residues: 792 helix: -1.27 (0.56), residues: 102 sheet: -1.97 (0.42), residues: 144 loop : -3.12 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 76 HIS 0.000 0.000 HIS A 83 PHE 0.008 0.002 PHE B 147 TYR 0.033 0.002 TYR C 138 ARG 0.002 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 24 time to evaluate : 0.679 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 46 average time/residue: 0.0980 time to fit residues: 7.9567 Evaluate side-chains 28 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 16 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0551 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6282 Z= 0.220 Angle : 0.741 8.109 8580 Z= 0.364 Chirality : 0.049 0.139 966 Planarity : 0.006 0.040 1128 Dihedral : 4.415 12.843 894 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 5.13 % Allowed : 17.63 % Favored : 77.24 % 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: -3.43 (0.27), residues: 792 helix: 0.48 (0.70), residues: 66 sheet: -1.94 (0.56), residues: 96 loop : -2.92 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 76 HIS 0.007 0.002 HIS F 62 PHE 0.019 0.002 PHE D 147 TYR 0.019 0.002 TYR F 138 ARG 0.010 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 18 time to evaluate : 0.664 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 31 residues processed: 48 average time/residue: 0.1324 time to fit residues: 9.6803 Evaluate side-chains 41 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 10 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0010 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0518 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6282 Z= 0.173 Angle : 0.666 7.844 8580 Z= 0.319 Chirality : 0.046 0.117 966 Planarity : 0.006 0.040 1128 Dihedral : 4.021 11.528 894 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.85 % Allowed : 21.15 % Favored : 75.00 % 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: -3.48 (0.26), residues: 792 helix: 0.39 (0.66), residues: 66 sheet: -1.97 (0.56), residues: 96 loop : -2.95 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 76 HIS 0.002 0.001 HIS C 62 PHE 0.007 0.001 PHE E 147 TYR 0.015 0.002 TYR A 138 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 20 time to evaluate : 0.637 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 42 average time/residue: 0.0964 time to fit residues: 7.0822 Evaluate side-chains 28 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 10 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0570 chunk 42 optimal weight: 0.0010 chunk 63 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 overall best weight: 0.0850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0451 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6282 Z= 0.163 Angle : 0.644 7.844 8580 Z= 0.306 Chirality : 0.047 0.133 966 Planarity : 0.005 0.035 1128 Dihedral : 3.785 11.910 894 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.37 % Allowed : 22.92 % Favored : 73.72 % 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: -3.54 (0.26), residues: 792 helix: -0.38 (0.61), residues: 66 sheet: -1.90 (0.56), residues: 96 loop : -2.93 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 76 HIS 0.001 0.000 HIS A 62 PHE 0.008 0.001 PHE F 147 TYR 0.013 0.001 TYR B 138 ARG 0.004 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 11 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 32 average time/residue: 0.1061 time to fit residues: 6.1254 Evaluate side-chains 23 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 7 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 42 optimal weight: 0.0270 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0560 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6282 Z= 0.173 Angle : 0.662 7.852 8580 Z= 0.316 Chirality : 0.047 0.153 966 Planarity : 0.005 0.037 1128 Dihedral : 3.838 11.217 894 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.37 % Allowed : 22.76 % Favored : 73.88 % 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: -3.51 (0.26), residues: 792 helix: -0.17 (0.63), residues: 66 sheet: -1.69 (0.58), residues: 96 loop : -2.96 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 76 HIS 0.003 0.001 HIS E 62 PHE 0.012 0.001 PHE D 147 TYR 0.014 0.002 TYR D 138 ARG 0.005 0.001 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 12 time to evaluate : 0.701 Fit side-chains outliers start: 21 outliers final: 20 residues processed: 33 average time/residue: 0.0939 time to fit residues: 5.8471 Evaluate side-chains 24 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 4 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 66 optimal weight: 0.0030 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0615 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6282 Z= 0.169 Angle : 0.651 7.562 8580 Z= 0.311 Chirality : 0.047 0.151 966 Planarity : 0.005 0.042 1128 Dihedral : 3.864 11.268 894 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.85 % Allowed : 23.08 % Favored : 73.08 % 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 (0.26), residues: 792 helix: -0.31 (0.61), residues: 66 sheet: -0.51 (0.54), residues: 84 loop : -2.92 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 76 HIS 0.002 0.001 HIS B 62 PHE 0.009 0.001 PHE A 147 TYR 0.014 0.002 TYR D 48 ARG 0.002 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 6 time to evaluate : 0.698 Fit side-chains REVERT: A 74 GLN cc_start: 0.1308 (OUTLIER) cc_final: 0.0695 (pt0) outliers start: 24 outliers final: 20 residues processed: 30 average time/residue: 0.1472 time to fit residues: 7.0886 Evaluate side-chains 25 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 4 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0766 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6282 Z= 0.210 Angle : 0.709 8.594 8580 Z= 0.344 Chirality : 0.048 0.150 966 Planarity : 0.006 0.068 1128 Dihedral : 4.098 11.262 894 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 3.69 % Allowed : 23.56 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.26), residues: 792 helix: -0.33 (0.62), residues: 66 sheet: -0.92 (0.46), residues: 126 loop : -3.03 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 76 HIS 0.006 0.002 HIS B 62 PHE 0.012 0.002 PHE D 147 TYR 0.015 0.002 TYR D 132 ARG 0.010 0.001 ARG F 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 6 time to evaluate : 0.655 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 29 average time/residue: 0.0971 time to fit residues: 5.3763 Evaluate side-chains 27 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 4 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 70 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 overall best weight: 0.0672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.298481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.278474 restraints weight = 23083.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.278474 restraints weight = 26801.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.278474 restraints weight = 26801.813| |-----------------------------------------------------------------------------| r_work (final): 0.5256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0893 moved from start: 0.8221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6282 Z= 0.160 Angle : 0.645 7.893 8580 Z= 0.307 Chirality : 0.047 0.142 966 Planarity : 0.006 0.043 1128 Dihedral : 3.856 12.456 894 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.37 % Allowed : 23.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.26), residues: 792 helix: -0.55 (0.60), residues: 66 sheet: -1.81 (0.50), residues: 102 loop : -2.85 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 76 HIS 0.000 0.000 HIS A 83 PHE 0.005 0.001 PHE A 147 TYR 0.011 0.002 TYR A 138 ARG 0.015 0.001 ARG F 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.70 seconds wall clock time: 33 minutes 43.95 seconds (2023.95 seconds total)