Starting phenix.real_space_refine on Fri May 9 14:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw6_39624/05_2025/8yw6_39624.cif" } resolution = 3.18 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'PC8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 2.94, per 1000 atoms: 1.07 Number of scatterers: 2747 At special positions: 0 Unit cell: (78.66, 79.23, 91.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 300.4 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 61.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.708A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 125 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.585A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 777 1.43 - 1.56: 1581 1.56 - 1.68: 19 1.68 - 1.81: 28 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.10e-02 8.26e+03 8.47e+01 bond pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.433 -0.099 1.10e-02 8.26e+03 8.17e+01 bond pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.23e+01 bond pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.06e+01 bond pdb=" OB2 CDL B 202 " pdb=" PB2 CDL B 202 " ideal model delta sigma weight residual 1.579 1.669 -0.090 1.50e-02 4.44e+03 3.62e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 3727 3.23 - 6.46: 51 6.46 - 9.69: 7 9.69 - 12.93: 1 12.93 - 16.16: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 202 " pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 111.33 118.92 -7.59 1.32e+00 5.72e-01 3.30e+01 angle pdb=" O3 PC8 B 201 " pdb=" P1 PC8 B 201 " pdb=" O4 PC8 B 201 " ideal model delta sigma weight residual 93.28 109.44 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C31 CDL B 202 " pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.39 -8.75 1.65e+00 3.69e-01 2.83e+01 angle pdb=" C71 CDL B 202 " pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.11 -8.47 1.65e+00 3.69e-01 2.65e+01 angle pdb=" C11 CDL B 202 " pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 111.33 117.31 -5.98 1.32e+00 5.72e-01 2.05e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 1619 32.93 - 65.85: 70 65.85 - 98.78: 3 98.78 - 131.71: 0 131.71 - 164.63: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" O5 PC8 B 201 " pdb=" C7 PC8 B 201 " pdb=" C8 PC8 B 201 " pdb=" O7 PC8 B 201 " ideal model delta sinusoidal sigma weight residual 52.89 -142.48 -164.63 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA5 CDL B 202 " pdb=" CA4 CDL B 202 " pdb=" OA6 CDL B 202 " pdb=" CA6 CDL B 202 " ideal model delta sinusoidal sigma weight residual 168.24 75.71 92.53 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CA TYR C 35 " pdb=" C TYR C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 285 0.052 - 0.104: 70 0.104 - 0.155: 26 0.155 - 0.207: 7 0.207 - 0.259: 4 Chirality restraints: 392 Sorted by residual: chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN A 77 " pdb=" N ASN A 77 " pdb=" C ASN A 77 " pdb=" CB ASN A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ARG B 62 " pdb=" N ARG B 62 " pdb=" C ARG B 62 " pdb=" CB ARG B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 76 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG A 76 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG A 76 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 77 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 25 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 53 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C SER C 53 " -0.024 2.00e-02 2.50e+03 pdb=" O SER C 53 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1003 2.90 - 3.40: 2614 3.40 - 3.90: 4765 3.90 - 4.40: 5264 4.40 - 4.90: 8613 Nonbonded interactions: 22259 Sorted by model distance: nonbonded pdb=" OD2 ASP C 73 " pdb=" NZ LYS C 76 " model vdw 2.395 3.120 nonbonded pdb=" O4 PC8 B 201 " pdb=" O7 PC8 B 201 " model vdw 2.468 2.432 nonbonded pdb=" O GLU C 31 " pdb=" OG SER C 53 " model vdw 2.547 3.040 nonbonded pdb=" OD1 ASP B 18 " pdb=" NH2 ARG B 39 " model vdw 2.555 3.120 nonbonded pdb=" C1 PC8 B 201 " pdb=" C3 PC8 B 201 " model vdw 2.609 3.088 ... (remaining 22254 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.340 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.012 0.105 2815 Z= 0.693 Angle : 1.003 16.157 3789 Z= 0.596 Chirality : 0.061 0.259 392 Planarity : 0.004 0.042 464 Dihedral : 16.353 164.632 1076 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 1.48 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.47), residues: 327 helix: 0.65 (0.36), residues: 176 sheet: -0.31 (0.70), residues: 55 loop : 1.64 (0.73), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 102 HIS 0.001 0.000 HIS A 26 PHE 0.001 0.000 PHE A 66 TYR 0.008 0.000 TYR C 95 ARG 0.001 0.000 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.16961 ( 175) hydrogen bonds : angle 6.83407 ( 489) SS BOND : bond 0.01024 ( 1) SS BOND : angle 0.98399 ( 2) covalent geometry : bond 0.01172 ( 2814) covalent geometry : angle 1.00332 ( 3787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.304 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.2733 time to fit residues: 9.9628 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.187821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131395 restraints weight = 2802.136| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.39 r_work: 0.3255 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2815 Z= 0.130 Angle : 0.490 5.586 3789 Z= 0.260 Chirality : 0.041 0.133 392 Planarity : 0.004 0.037 464 Dihedral : 17.071 171.517 476 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.46), residues: 327 helix: 2.38 (0.38), residues: 177 sheet: 0.10 (0.69), residues: 49 loop : 1.72 (0.65), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.015 0.001 TYR C 95 ARG 0.008 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 175) hydrogen bonds : angle 4.37472 ( 489) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.75453 ( 2) covalent geometry : bond 0.00299 ( 2814) covalent geometry : angle 0.49018 ( 3787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.313 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.1852 time to fit residues: 4.5527 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.182909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127293 restraints weight = 2788.996| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.31 r_work: 0.3215 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2815 Z= 0.146 Angle : 0.477 6.081 3789 Z= 0.251 Chirality : 0.042 0.141 392 Planarity : 0.004 0.036 464 Dihedral : 15.278 152.017 476 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 4.81 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.47), residues: 327 helix: 2.46 (0.39), residues: 179 sheet: 0.01 (0.68), residues: 51 loop : 1.53 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.014 0.002 PHE A 69 TYR 0.015 0.001 TYR C 95 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 175) hydrogen bonds : angle 4.11413 ( 489) SS BOND : bond 0.00373 ( 1) SS BOND : angle 0.56132 ( 2) covalent geometry : bond 0.00349 ( 2814) covalent geometry : angle 0.47694 ( 3787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.300 Fit side-chains REVERT: C 32 ARG cc_start: 0.7751 (mmp80) cc_final: 0.7491 (mmp80) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.1968 time to fit residues: 6.6548 Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 6 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130801 restraints weight = 2838.797| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.33 r_work: 0.3262 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2815 Z= 0.102 Angle : 0.421 5.249 3789 Z= 0.221 Chirality : 0.039 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 13.919 143.936 476 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 6.30 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.46), residues: 327 helix: 2.83 (0.39), residues: 175 sheet: 0.14 (0.68), residues: 50 loop : 1.46 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 PHE 0.010 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 175) hydrogen bonds : angle 3.69225 ( 489) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.73307 ( 2) covalent geometry : bond 0.00235 ( 2814) covalent geometry : angle 0.42106 ( 3787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1644 time to fit residues: 5.0050 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.183091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127823 restraints weight = 2827.272| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.34 r_work: 0.3229 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.120 Angle : 0.438 5.300 3789 Z= 0.230 Chirality : 0.040 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 13.604 140.944 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.37 % Allowed : 8.89 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.46), residues: 327 helix: 2.73 (0.39), residues: 176 sheet: 0.22 (0.67), residues: 50 loop : 1.55 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.014 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 175) hydrogen bonds : angle 3.71478 ( 489) SS BOND : bond 0.00297 ( 1) SS BOND : angle 0.48353 ( 2) covalent geometry : bond 0.00283 ( 2814) covalent geometry : angle 0.43808 ( 3787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.265 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1986 time to fit residues: 5.7907 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.183514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127940 restraints weight = 2819.333| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.34 r_work: 0.3234 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.116 Angle : 0.434 5.262 3789 Z= 0.228 Chirality : 0.040 0.127 392 Planarity : 0.004 0.033 464 Dihedral : 13.306 139.130 476 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.46), residues: 327 helix: 2.77 (0.39), residues: 175 sheet: 0.24 (0.68), residues: 50 loop : 1.47 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.012 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 175) hydrogen bonds : angle 3.70846 ( 489) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.63959 ( 2) covalent geometry : bond 0.00272 ( 2814) covalent geometry : angle 0.43411 ( 3787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.328 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2009 time to fit residues: 5.8469 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.184081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129536 restraints weight = 2881.531| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.32 r_work: 0.3248 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2815 Z= 0.103 Angle : 0.419 5.221 3789 Z= 0.219 Chirality : 0.039 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 12.523 136.433 476 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 10.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.03 (0.47), residues: 327 helix: 2.87 (0.39), residues: 175 sheet: 0.37 (0.68), residues: 50 loop : 1.50 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 PHE 0.011 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 175) hydrogen bonds : angle 3.63492 ( 489) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.47094 ( 2) covalent geometry : bond 0.00239 ( 2814) covalent geometry : angle 0.41916 ( 3787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.300 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.2037 time to fit residues: 5.6416 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.184831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130571 restraints weight = 2825.597| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.31 r_work: 0.3261 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2815 Z= 0.097 Angle : 0.414 5.148 3789 Z= 0.216 Chirality : 0.039 0.129 392 Planarity : 0.004 0.033 464 Dihedral : 12.271 134.445 476 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.47), residues: 327 helix: 2.90 (0.39), residues: 175 sheet: 0.58 (0.69), residues: 50 loop : 1.51 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 PHE 0.010 0.001 PHE A 69 TYR 0.012 0.001 TYR C 95 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 175) hydrogen bonds : angle 3.56753 ( 489) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.47505 ( 2) covalent geometry : bond 0.00221 ( 2814) covalent geometry : angle 0.41403 ( 3787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2082 time to fit residues: 5.8013 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127454 restraints weight = 2817.578| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.32 r_work: 0.3221 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.120 Angle : 0.440 5.250 3789 Z= 0.230 Chirality : 0.040 0.127 392 Planarity : 0.004 0.033 464 Dihedral : 12.466 135.920 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.37 % Allowed : 10.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.47), residues: 327 helix: 2.78 (0.39), residues: 175 sheet: 0.56 (0.69), residues: 50 loop : 1.50 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 PHE 0.013 0.001 PHE A 69 TYR 0.013 0.001 TYR C 95 ARG 0.004 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 175) hydrogen bonds : angle 3.68959 ( 489) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.52996 ( 2) covalent geometry : bond 0.00287 ( 2814) covalent geometry : angle 0.44010 ( 3787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.279 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.1520 time to fit residues: 4.3171 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 65.9778 > 50: distance: 56 - 80: 15.917 distance: 67 - 91: 16.282 distance: 71 - 99: 20.522 distance: 75 - 80: 15.306 distance: 76 - 110: 15.172 distance: 80 - 81: 21.113 distance: 81 - 82: 22.461 distance: 81 - 84: 17.786 distance: 82 - 83: 23.122 distance: 82 - 91: 18.909 distance: 83 - 121: 17.115 distance: 84 - 85: 3.984 distance: 85 - 86: 30.703 distance: 85 - 87: 7.989 distance: 86 - 88: 15.445 distance: 87 - 89: 13.837 distance: 88 - 90: 3.455 distance: 89 - 90: 20.596 distance: 91 - 92: 25.689 distance: 92 - 93: 11.848 distance: 92 - 95: 17.351 distance: 93 - 94: 11.385 distance: 93 - 99: 20.488 distance: 94 - 126: 14.133 distance: 95 - 96: 15.847 distance: 96 - 97: 8.411 distance: 97 - 98: 24.503 distance: 99 - 100: 15.504 distance: 100 - 101: 3.915 distance: 100 - 103: 16.857 distance: 101 - 102: 14.441 distance: 101 - 110: 22.487 distance: 102 - 138: 28.616 distance: 103 - 104: 9.697 distance: 104 - 105: 12.486 distance: 105 - 106: 3.342 distance: 106 - 107: 6.971 distance: 107 - 108: 15.240 distance: 107 - 109: 16.491 distance: 110 - 111: 8.113 distance: 111 - 112: 14.481 distance: 111 - 114: 9.721 distance: 112 - 113: 13.861 distance: 112 - 121: 10.350 distance: 113 - 147: 34.989 distance: 114 - 115: 5.401 distance: 115 - 116: 8.721 distance: 115 - 117: 4.804 distance: 116 - 118: 13.301 distance: 118 - 120: 12.027 distance: 119 - 120: 6.076 distance: 121 - 122: 12.215 distance: 122 - 123: 12.825 distance: 122 - 125: 11.757 distance: 123 - 124: 38.756 distance: 123 - 126: 18.747 distance: 126 - 127: 12.515 distance: 127 - 128: 16.219 distance: 127 - 130: 24.179 distance: 128 - 129: 27.487 distance: 128 - 138: 18.752 distance: 130 - 131: 14.568 distance: 131 - 132: 23.639 distance: 131 - 133: 23.679 distance: 132 - 134: 19.440 distance: 133 - 135: 4.885 distance: 134 - 136: 25.352 distance: 135 - 136: 9.973 distance: 136 - 137: 6.524 distance: 138 - 139: 13.377 distance: 139 - 140: 21.919 distance: 139 - 142: 34.908 distance: 140 - 141: 3.500 distance: 140 - 147: 11.247 distance: 142 - 143: 40.303 distance: 143 - 144: 26.020 distance: 144 - 145: 3.743 distance: 145 - 146: 17.607 distance: 147 - 148: 8.832 distance: 148 - 149: 5.436 distance: 148 - 151: 11.838 distance: 149 - 150: 6.527 distance: 149 - 154: 25.635 distance: 151 - 152: 14.568 distance: 151 - 153: 35.273 distance: 154 - 155: 8.458 distance: 155 - 156: 54.019 distance: 155 - 158: 19.030 distance: 156 - 157: 18.803 distance: 156 - 163: 25.506 distance: 158 - 159: 26.707 distance: 159 - 160: 36.508 distance: 160 - 161: 10.261 distance: 160 - 162: 21.441 distance: 163 - 164: 49.142 distance: 163 - 169: 12.856 distance: 164 - 165: 60.502 distance: 164 - 167: 3.385 distance: 165 - 166: 22.576 distance: 165 - 170: 27.338 distance: 167 - 168: 41.081 distance: 168 - 169: 40.263