Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2itb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 241 and 0 Target number of residues in the AU: 241 Target solvent content: 0.6396 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 53.913 3.401 Wilson plot Bfac: 71.79 5306 reflections ( 99.72 % complete ) and 0 restraints for refining 3670 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3516 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2840 (Rfree = 0.000) for 3670 atoms. Found 12 (27 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.98 Search for helices and strands: 0 residues in 0 chains, 3762 seeds are put forward NCS extension: 0 residues added, 3762 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 7 peptides. Score 0.220 Round 2: 148 peptides, 30 chains. Longest chain 8 peptides. Score 0.308 Round 3: 170 peptides, 32 chains. Longest chain 10 peptides. Score 0.371 Round 4: 183 peptides, 32 chains. Longest chain 9 peptides. Score 0.427 Round 5: 185 peptides, 31 chains. Longest chain 10 peptides. Score 0.453 Taking the results from Round 5 Chains 31, Residues 154, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6897 restraints for refining 2996 atoms. 6284 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3256 (Rfree = 0.000) for 2996 atoms. Found 14 (22 requested) and removed 23 (11 requested) atoms. Cycle 2: After refmac, R = 0.2868 (Rfree = 0.000) for 2966 atoms. Found 9 (22 requested) and removed 14 (11 requested) atoms. Cycle 3: After refmac, R = 0.2827 (Rfree = 0.000) for 2946 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 4: After refmac, R = 0.2725 (Rfree = 0.000) for 2932 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2681 (Rfree = 0.000) for 2919 atoms. Found 0 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.92 Search for helices and strands: 0 residues in 0 chains, 3074 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3086 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 8 peptides. Score 0.283 Round 2: 178 peptides, 33 chains. Longest chain 9 peptides. Score 0.387 Round 3: 185 peptides, 34 chains. Longest chain 11 peptides. Score 0.399 Round 4: 192 peptides, 31 chains. Longest chain 14 peptides. Score 0.481 Round 5: 189 peptides, 29 chains. Longest chain 18 peptides. Score 0.503 Taking the results from Round 5 Chains 29, Residues 160, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6871 restraints for refining 2910 atoms. 6260 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2998 (Rfree = 0.000) for 2910 atoms. Found 10 (21 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2892 (Rfree = 0.000) for 2891 atoms. Found 3 (21 requested) and removed 12 (10 requested) atoms. Cycle 8: After refmac, R = 0.2726 (Rfree = 0.000) for 2879 atoms. Found 1 (21 requested) and removed 12 (10 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2669 (Rfree = 0.000) for 2858 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Cycle 10: After refmac, R = 0.2741 (Rfree = 0.000) for 2849 atoms. Found 0 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2987 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3004 seeds are put forward Round 1: 138 peptides, 27 chains. Longest chain 9 peptides. Score 0.320 Round 2: 172 peptides, 32 chains. Longest chain 11 peptides. Score 0.380 Round 3: 177 peptides, 32 chains. Longest chain 11 peptides. Score 0.401 Round 4: 175 peptides, 31 chains. Longest chain 15 peptides. Score 0.411 Round 5: 178 peptides, 31 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 5 Chains 31, Residues 147, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 6721 restraints for refining 2873 atoms. 6145 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3074 (Rfree = 0.000) for 2873 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2896 (Rfree = 0.000) for 2868 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2851 (Rfree = 0.000) for 2862 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2823 (Rfree = 0.000) for 2855 atoms. Found 3 (21 requested) and removed 10 (10 requested) atoms. Cycle 15: After refmac, R = 0.2817 (Rfree = 0.000) for 2847 atoms. Found 1 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 2958 seeds are put forward NCS extension: 0 residues added, 2958 seeds are put forward Round 1: 159 peptides, 35 chains. Longest chain 7 peptides. Score 0.261 Round 2: 164 peptides, 31 chains. Longest chain 12 peptides. Score 0.363 Round 3: 173 peptides, 33 chains. Longest chain 11 peptides. Score 0.365 Round 4: 171 peptides, 29 chains. Longest chain 14 peptides. Score 0.430 Round 5: 155 peptides, 29 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 4 Chains 29, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5306 reflections ( 99.72 % complete ) and 7137 restraints for refining 2958 atoms. 6598 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3049 (Rfree = 0.000) for 2958 atoms. Found 8 (22 requested) and removed 14 (11 requested) atoms. Cycle 17: After refmac, R = 0.2928 (Rfree = 0.000) for 2947 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2862 (Rfree = 0.000) for 2937 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2813 (Rfree = 0.000) for 2924 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2791 (Rfree = 0.000) for 2912 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 3026 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3044 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 8 peptides. Score 0.285 Round 2: 167 peptides, 31 chains. Longest chain 9 peptides. Score 0.376 Round 3: 171 peptides, 30 chains. Longest chain 9 peptides. Score 0.412 Round 4: 181 peptides, 31 chains. Longest chain 12 peptides. Score 0.436 Round 5: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 5 Chains 28, Residues 142, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5306 reflections ( 99.72 % complete ) and 7006 restraints for refining 2972 atoms. 6416 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3074 (Rfree = 0.000) for 2972 atoms. Found 15 (22 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2921 (Rfree = 0.000) for 2970 atoms. Found 1 (22 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.2885 (Rfree = 0.000) for 2957 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.2905 (Rfree = 0.000) for 2947 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2877 (Rfree = 0.000) for 2938 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 3058 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3077 seeds are put forward Round 1: 141 peptides, 31 chains. Longest chain 8 peptides. Score 0.254 Round 2: 166 peptides, 31 chains. Longest chain 13 peptides. Score 0.372 Round 3: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.306 Round 4: 166 peptides, 31 chains. Longest chain 13 peptides. Score 0.372 Round 5: 158 peptides, 28 chains. Longest chain 15 peptides. Score 0.393 Taking the results from Round 5 Chains 28, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7338 restraints for refining 2991 atoms. 6846 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3092 (Rfree = 0.000) for 2991 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 27: After refmac, R = 0.2975 (Rfree = 0.000) for 2986 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2947 (Rfree = 0.000) for 2976 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2961 (Rfree = 0.000) for 2967 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2929 (Rfree = 0.000) for 2960 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 3080 seeds are put forward NCS extension: 0 residues added, 3080 seeds are put forward Round 1: 106 peptides, 25 chains. Longest chain 5 peptides. Score 0.200 Round 2: 134 peptides, 27 chains. Longest chain 7 peptides. Score 0.301 Round 3: 131 peptides, 26 chains. Longest chain 10 peptides. Score 0.307 Round 4: 131 peptides, 24 chains. Longest chain 9 peptides. Score 0.348 Round 5: 145 peptides, 25 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 5 Chains 25, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7189 restraints for refining 2947 atoms. 6734 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3263 (Rfree = 0.000) for 2947 atoms. Found 14 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.3173 (Rfree = 0.000) for 2949 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.3112 (Rfree = 0.000) for 2940 atoms. Found 4 (22 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.3087 (Rfree = 0.000) for 2932 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.3077 (Rfree = 0.000) for 2922 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 3034 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3047 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 8 peptides. Score 0.233 Round 2: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.273 Round 3: 123 peptides, 24 chains. Longest chain 7 peptides. Score 0.309 Round 4: 132 peptides, 24 chains. Longest chain 11 peptides. Score 0.352 Round 5: 127 peptides, 25 chains. Longest chain 9 peptides. Score 0.308 Taking the results from Round 4 Chains 24, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5306 reflections ( 99.72 % complete ) and 7202 restraints for refining 2933 atoms. 6794 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3177 (Rfree = 0.000) for 2933 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 37: After refmac, R = 0.3050 (Rfree = 0.000) for 2930 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.3021 (Rfree = 0.000) for 2922 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.3023 (Rfree = 0.000) for 2912 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.3021 (Rfree = 0.000) for 2902 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 3018 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3030 seeds are put forward Round 1: 113 peptides, 26 chains. Longest chain 7 peptides. Score 0.216 Round 2: 131 peptides, 27 chains. Longest chain 7 peptides. Score 0.286 Round 3: 144 peptides, 29 chains. Longest chain 7 peptides. Score 0.309 Round 4: 136 peptides, 27 chains. Longest chain 8 peptides. Score 0.311 Round 5: 142 peptides, 27 chains. Longest chain 9 peptides. Score 0.339 Taking the results from Round 5 Chains 27, Residues 115, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5306 reflections ( 99.72 % complete ) and 7233 restraints for refining 2978 atoms. 6763 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3146 (Rfree = 0.000) for 2978 atoms. Found 13 (22 requested) and removed 17 (11 requested) atoms. Cycle 42: After refmac, R = 0.3011 (Rfree = 0.000) for 2973 atoms. Found 6 (22 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2972 (Rfree = 0.000) for 2967 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2940 (Rfree = 0.000) for 2956 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2933 (Rfree = 0.000) for 2946 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 3033 seeds are put forward NCS extension: 0 residues added, 3033 seeds are put forward Round 1: 108 peptides, 24 chains. Longest chain 7 peptides. Score 0.233 Round 2: 126 peptides, 25 chains. Longest chain 9 peptides. Score 0.303 Round 3: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.346 Round 4: 120 peptides, 21 chains. Longest chain 10 peptides. Score 0.357 Round 5: 117 peptides, 23 chains. Longest chain 8 peptides. Score 0.300 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 99, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2itb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 5306 reflections ( 99.72 % complete ) and 7386 restraints for refining 2955 atoms. 7011 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3051 (Rfree = 0.000) for 2955 atoms. Found 0 (22 requested) and removed 6 (11 requested) atoms. Cycle 47: After refmac, R = 0.2997 (Rfree = 0.000) for 2946 atoms. Found 0 (22 requested) and removed 1 (11 requested) atoms. Cycle 48: After refmac, R = 0.2956 (Rfree = 0.000) for 2945 atoms. Found 0 (22 requested) and removed 0 (11 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2920 (Rfree = 0.000) for 2945 atoms. Found 0 (22 requested) and removed 2 (11 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:18:12 GMT 2018 Job finished. TimeTaking 50.25