Starting phenix.real_space_refine on Tue Apr 29 05:36:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.map" model { file = "/net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i65_52650/04_2025/9i65_52650.cif" } resolution = 4.1 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= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 5427 2.51 5 N 1305 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "L" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 937 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 124} Time building chain proxies: 5.68, per 1000 atoms: 0.67 Number of scatterers: 8433 At special positions: 0 Unit cell: (63.9, 63.9, 315.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1692 8.00 N 1305 7.00 C 5427 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: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 27 sheets defined 3.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'G' and resid 84 through 88 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.520A pdb=" N LEU L 87 " --> pdb=" O GLN L 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 42 removed outlier: 4.116A pdb=" N MET M 41 " --> pdb=" O THR M 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE M 42 " --> pdb=" O ALA M 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 38 through 42' Processing helix chain 'M' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.520A pdb=" N THR E 133 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.865A pdb=" N VAL E 21 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 108 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 50 removed outlier: 4.172A pdb=" N THR E 47 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 49 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'F' and resid 17 through 18 removed outlier: 3.895A pdb=" N THR F 126 " --> pdb=" O THR F 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 54 through 56 removed outlier: 4.048A pdb=" N VAL F 108 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE F 37 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR F 106 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL F 76 " --> pdb=" O GLN F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 9 through 11 Processing sheet with id=AA9, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AB1, first strand: chain 'G' and resid 21 through 35 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 60 through 61 current: chain 'G' and resid 81 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 81 through 82 current: chain 'J' and resid 54 through 56 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 56 current: chain 'J' and resid 81 through 83 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 81 through 83 current: chain 'M' and resid 81 through 82 Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.521A pdb=" N THR H 133 " --> pdb=" O VAL H 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.841A pdb=" N VAL H 108 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 109 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL H 76 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.905A pdb=" N ILE H 49 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AB8, first strand: chain 'I' and resid 22 through 35 removed outlier: 4.099A pdb=" N VAL I 108 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL I 76 " --> pdb=" O GLN I 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AC1, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.824A pdb=" N THR J 126 " --> pdb=" O THR J 18 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.550A pdb=" N VAL K 11 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 60 through 61 removed outlier: 7.346A pdb=" N VAL K 21 " --> pdb=" O THR K 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR K 122 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL K 108 " --> pdb=" O ALA K 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.734A pdb=" N ILE K 49 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.505A pdb=" N VAL L 11 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 133 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.721A pdb=" N VAL L 21 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL L 108 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE L 37 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR L 106 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 76 " --> pdb=" O GLN L 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 48 through 50 removed outlier: 3.638A pdb=" N ILE L 49 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 9 through 12 212 hydrogen bonds defined for protein. 525 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: 2.13 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2691 1.34 - 1.46: 1658 1.46 - 1.57: 4228 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 8595 Sorted by residual: bond pdb=" CA ILE L 49 " pdb=" CB ILE L 49 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.23e-02 6.61e+03 2.42e+00 bond pdb=" CA ALA K 51 " pdb=" C ALA K 51 " ideal model delta sigma weight residual 1.522 1.501 0.020 1.72e-02 3.38e+03 1.39e+00 bond pdb=" N ILE L 37 " pdb=" CA ILE L 37 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.04e+00 bond pdb=" N GLY G 80 " pdb=" CA GLY G 80 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.03e+00 bond pdb=" C GLY F 44 " pdb=" N GLY F 45 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.51e-01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11529 1.80 - 3.60: 329 3.60 - 5.40: 26 5.40 - 7.19: 4 7.19 - 8.99: 1 Bond angle restraints: 11889 Sorted by residual: angle pdb=" N ILE L 37 " pdb=" CA ILE L 37 " pdb=" C ILE L 37 " ideal model delta sigma weight residual 106.21 111.79 -5.58 1.07e+00 8.73e-01 2.72e+01 angle pdb=" C ASP E 57 " pdb=" N ALA E 58 " pdb=" CA ALA E 58 " ideal model delta sigma weight residual 121.90 116.87 5.03 1.26e+00 6.30e-01 1.59e+01 angle pdb=" N VAL H 93 " pdb=" CA VAL H 93 " pdb=" C VAL H 93 " ideal model delta sigma weight residual 113.53 109.79 3.74 9.80e-01 1.04e+00 1.45e+01 angle pdb=" C VAL I 3 " pdb=" N ILE I 4 " pdb=" CA ILE I 4 " ideal model delta sigma weight residual 121.97 127.73 -5.76 1.80e+00 3.09e-01 1.02e+01 angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 113.53 110.63 2.90 9.80e-01 1.04e+00 8.73e+00 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4695 16.11 - 32.23: 302 32.23 - 48.34: 60 48.34 - 64.46: 4 64.46 - 80.57: 6 Dihedral angle restraints: 5067 sinusoidal: 1629 harmonic: 3438 Sorted by residual: dihedral pdb=" CA GLU L 104 " pdb=" C GLU L 104 " pdb=" N GLY L 105 " pdb=" CA GLY L 105 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR I 48 " pdb=" C THR I 48 " pdb=" N ILE I 49 " pdb=" CA ILE I 49 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA F 52 " pdb=" C ALA F 52 " pdb=" N SER F 53 " pdb=" CA SER F 53 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1299 0.058 - 0.116: 263 0.116 - 0.174: 29 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CB ILE L 37 " pdb=" CA ILE L 37 " pdb=" CG1 ILE L 37 " pdb=" CG2 ILE L 37 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE E 49 " pdb=" CA ILE E 49 " pdb=" CG1 ILE E 49 " pdb=" CG2 ILE E 49 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL J 108 " pdb=" N VAL J 108 " pdb=" C VAL J 108 " pdb=" CB VAL J 108 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1590 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 49 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.88e+00 pdb=" N PRO G 50 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 50 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 50 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 49 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO F 50 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 101 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C ASP I 101 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP I 101 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE I 102 " -0.010 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 410 2.71 - 3.26: 8515 3.26 - 3.80: 13037 3.80 - 4.35: 14900 4.35 - 4.90: 26185 Nonbonded interactions: 63047 Sorted by model distance: nonbonded pdb=" OG1 THR G 29 " pdb=" OG1 THR G 114 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR M 29 " pdb=" OG1 THR M 114 " model vdw 2.171 3.040 nonbonded pdb=" O VAL F 103 " pdb=" OG1 THR F 106 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR G 25 " pdb=" OD1 ASP G 118 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR H 29 " pdb=" OG1 THR H 114 " model vdw 2.186 3.040 ... (remaining 63042 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.320 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8595 Z= 0.154 Angle : 0.656 8.993 11889 Z= 0.363 Chirality : 0.047 0.290 1593 Planarity : 0.005 0.055 1503 Dihedral : 11.378 80.571 2871 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.28 % Favored : 88.22 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.21 (0.22), residues: 567 loop : -3.05 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE I 54 TYR 0.010 0.001 TYR F 34 ARG 0.003 0.000 ARG L 32 Details of bonding type rmsd hydrogen bonds : bond 0.30744 ( 212) hydrogen bonds : angle 13.38678 ( 525) covalent geometry : bond 0.00326 ( 8595) covalent geometry : angle 0.65602 (11889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 22 ILE cc_start: 0.9057 (mt) cc_final: 0.8803 (tt) REVERT: G 22 ILE cc_start: 0.8532 (mp) cc_final: 0.7991 (tt) REVERT: G 104 GLU cc_start: 0.7984 (pm20) cc_final: 0.7738 (pm20) REVERT: H 56 ASP cc_start: 0.6365 (t0) cc_final: 0.6146 (m-30) REVERT: I 83 GLN cc_start: 0.8079 (mt0) cc_final: 0.7814 (mt0) REVERT: I 106 THR cc_start: 0.8895 (m) cc_final: 0.8652 (p) REVERT: L 16 VAL cc_start: 0.8275 (t) cc_final: 0.8043 (m) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1315 time to fit residues: 30.7364 Evaluate side-chains 84 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 59 optimal weight: 0.0050 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 ASN ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150079 restraints weight = 14148.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.148262 restraints weight = 21192.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.148784 restraints weight = 22877.032| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8595 Z= 0.147 Angle : 0.664 11.817 11889 Z= 0.335 Chirality : 0.049 0.191 1593 Planarity : 0.005 0.048 1503 Dihedral : 5.148 37.365 1260 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.86 % Favored : 88.64 % Rotamer: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.41 (0.23), residues: 504 loop : -2.40 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE L 102 TYR 0.009 0.001 TYR F 73 ARG 0.003 0.001 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 212) hydrogen bonds : angle 8.03170 ( 525) covalent geometry : bond 0.00337 ( 8595) covalent geometry : angle 0.66372 (11889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.935 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1276 time to fit residues: 20.6693 Evaluate side-chains 73 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.161583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145736 restraints weight = 14490.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.143797 restraints weight = 23658.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144371 restraints weight = 24505.374| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8595 Z= 0.161 Angle : 0.668 12.903 11889 Z= 0.334 Chirality : 0.049 0.174 1593 Planarity : 0.005 0.057 1503 Dihedral : 5.234 40.188 1260 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.70 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 1.26 (0.23), residues: 504 loop : -2.40 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE I 54 TYR 0.014 0.001 TYR K 34 ARG 0.002 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 212) hydrogen bonds : angle 6.99785 ( 525) covalent geometry : bond 0.00395 ( 8595) covalent geometry : angle 0.66771 (11889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: J 4 ILE cc_start: 0.6657 (mp) cc_final: 0.6375 (mm) REVERT: M 49 ILE cc_start: 0.3475 (pt) cc_final: 0.3252 (pt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1282 time to fit residues: 18.4382 Evaluate side-chains 72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131569 restraints weight = 14670.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130519 restraints weight = 16472.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130159 restraints weight = 17973.909| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8595 Z= 0.304 Angle : 0.806 11.100 11889 Z= 0.406 Chirality : 0.052 0.200 1593 Planarity : 0.006 0.051 1503 Dihedral : 6.243 44.036 1260 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.87 % Favored : 84.71 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1197 helix: None (None), residues: 0 sheet: 0.60 (0.22), residues: 504 loop : -2.75 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE G 54 TYR 0.021 0.003 TYR L 73 ARG 0.004 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 212) hydrogen bonds : angle 7.50816 ( 525) covalent geometry : bond 0.00728 ( 8595) covalent geometry : angle 0.80614 (11889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: E 62 VAL cc_start: 0.4889 (t) cc_final: 0.4538 (p) REVERT: F 22 ILE cc_start: 0.9539 (mt) cc_final: 0.9194 (tt) REVERT: J 4 ILE cc_start: 0.6599 (mp) cc_final: 0.6395 (mm) REVERT: K 41 MET cc_start: 0.4514 (pmm) cc_final: 0.3647 (ttt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1300 time to fit residues: 17.3150 Evaluate side-chains 67 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.0060 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137400 restraints weight = 14409.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136900 restraints weight = 15548.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136900 restraints weight = 16380.837| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8595 Z= 0.156 Angle : 0.693 11.041 11889 Z= 0.345 Chirality : 0.049 0.158 1593 Planarity : 0.005 0.045 1503 Dihedral : 5.665 46.746 1260 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.20 % Favored : 87.39 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1197 helix: None (None), residues: 0 sheet: 0.70 (0.22), residues: 504 loop : -2.47 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE H 54 TYR 0.016 0.001 TYR E 34 ARG 0.003 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 212) hydrogen bonds : angle 6.58616 ( 525) covalent geometry : bond 0.00384 ( 8595) covalent geometry : angle 0.69256 (11889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: E 62 VAL cc_start: 0.4787 (t) cc_final: 0.4421 (p) REVERT: J 4 ILE cc_start: 0.6545 (mp) cc_final: 0.6308 (mm) REVERT: J 41 MET cc_start: 0.2846 (ttp) cc_final: 0.2474 (ttp) REVERT: L 83 GLN cc_start: 0.8137 (mm110) cc_final: 0.7787 (mm-40) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1212 time to fit residues: 16.9728 Evaluate side-chains 72 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 116 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.159426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.145118 restraints weight = 14208.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.143739 restraints weight = 21015.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.143758 restraints weight = 23565.581| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8595 Z= 0.155 Angle : 0.686 14.124 11889 Z= 0.342 Chirality : 0.049 0.182 1593 Planarity : 0.005 0.046 1503 Dihedral : 5.520 47.872 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.45 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.68 (0.22), residues: 504 loop : -2.35 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE I 54 TYR 0.024 0.001 TYR K 34 ARG 0.002 0.000 ARG E 32 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 212) hydrogen bonds : angle 6.30090 ( 525) covalent geometry : bond 0.00379 ( 8595) covalent geometry : angle 0.68624 (11889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.940 Fit side-chains REVERT: J 4 ILE cc_start: 0.6554 (mp) cc_final: 0.6243 (mm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1360 time to fit residues: 17.0243 Evaluate side-chains 66 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.0050 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 95 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.149003 restraints weight = 14156.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146988 restraints weight = 24219.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.147466 restraints weight = 24090.560| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8595 Z= 0.112 Angle : 0.651 12.378 11889 Z= 0.323 Chirality : 0.048 0.171 1593 Planarity : 0.004 0.045 1503 Dihedral : 5.133 49.540 1260 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.53 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -1.00 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.95 (0.22), residues: 504 loop : -2.06 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE I 54 TYR 0.019 0.001 TYR E 34 ARG 0.002 0.000 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 212) hydrogen bonds : angle 5.71174 ( 525) covalent geometry : bond 0.00278 ( 8595) covalent geometry : angle 0.65051 (11889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.877 Fit side-chains REVERT: E 56 ASP cc_start: 0.7460 (t0) cc_final: 0.6632 (m-30) REVERT: J 4 ILE cc_start: 0.6516 (mp) cc_final: 0.6203 (mm) REVERT: L 82 LEU cc_start: 0.7998 (mt) cc_final: 0.7405 (tt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1308 time to fit residues: 17.5936 Evaluate side-chains 64 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN ** L 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135669 restraints weight = 14601.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135669 restraints weight = 15720.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135669 restraints weight = 15721.180| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8595 Z= 0.222 Angle : 0.742 11.536 11889 Z= 0.369 Chirality : 0.049 0.157 1593 Planarity : 0.005 0.048 1503 Dihedral : 5.690 48.620 1260 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.78 % Favored : 85.80 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -1.34 (0.25), residues: 1197 helix: None (None), residues: 0 sheet: 0.68 (0.22), residues: 504 loop : -2.26 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE H 54 TYR 0.029 0.002 TYR K 34 ARG 0.002 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 212) hydrogen bonds : angle 6.48911 ( 525) covalent geometry : bond 0.00543 ( 8595) covalent geometry : angle 0.74161 (11889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.858 Fit side-chains REVERT: G 79 ASN cc_start: 0.8468 (t0) cc_final: 0.7939 (t0) REVERT: H 67 VAL cc_start: 0.6957 (t) cc_final: 0.6405 (p) REVERT: J 59 ASP cc_start: 0.6063 (m-30) cc_final: 0.5679 (t0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1214 time to fit residues: 15.2856 Evaluate side-chains 63 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.856 > 50: distance: 83 - 113: 25.324 distance: 100 - 105: 9.672 distance: 105 - 106: 17.183 distance: 106 - 107: 4.552 distance: 106 - 109: 3.011 distance: 107 - 108: 8.323 distance: 107 - 113: 12.313 distance: 109 - 110: 14.308 distance: 110 - 112: 27.608 distance: 113 - 114: 20.064 distance: 114 - 115: 4.803 distance: 114 - 117: 25.627 distance: 115 - 116: 19.032 distance: 115 - 120: 24.496 distance: 117 - 118: 34.824 distance: 117 - 119: 17.339 distance: 122 - 127: 14.682 distance: 124 - 126: 6.721 distance: 127 - 128: 26.699 distance: 128 - 129: 34.546 distance: 128 - 131: 32.634 distance: 129 - 130: 11.215 distance: 129 - 136: 11.124 distance: 131 - 132: 22.554 distance: 132 - 133: 19.724 distance: 133 - 134: 39.218 distance: 133 - 135: 11.097 distance: 137 - 138: 15.508 distance: 137 - 140: 3.474 distance: 138 - 143: 23.809 distance: 140 - 141: 24.427 distance: 141 - 142: 25.954 distance: 144 - 145: 7.696 distance: 145 - 146: 11.019 distance: 145 - 150: 43.466 distance: 150 - 151: 14.743 distance: 151 - 152: 20.471 distance: 151 - 154: 51.081 distance: 152 - 153: 11.080 distance: 152 - 158: 14.251 distance: 154 - 155: 30.235 distance: 154 - 156: 18.403 distance: 158 - 159: 15.838 distance: 159 - 160: 13.312 distance: 160 - 161: 15.942 distance: 160 - 164: 15.733 distance: 162 - 163: 19.116 distance: 165 - 166: 17.355 distance: 166 - 167: 23.863 distance: 166 - 169: 18.020 distance: 169 - 170: 19.791 distance: 169 - 175: 16.519 distance: 170 - 171: 15.378 distance: 170 - 173: 15.184 distance: 171 - 172: 25.557 distance: 171 - 176: 22.083 distance: 173 - 174: 5.239 distance: 174 - 175: 6.814