null Mon 24 Dec 00:26:12 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:26:18 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/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-mrncs/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 245 and 0 Target number of residues in the AU: 245 Target solvent content: 0.6741 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-4.0-parrot-mrncs.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: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.70 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: 55.473 4.000 Wilson plot Bfac: 95.59 3709 reflections ( 99.52 % complete ) and 0 restraints for refining 3687 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3333 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3318 (Rfree = 0.000) for 3687 atoms. Found 17 (17 requested) and removed 98 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 3673 seeds are put forward NCS extension: 0 residues added, 3673 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 9 peptides. Score 0.276 Round 2: 188 peptides, 33 chains. Longest chain 11 peptides. Score 0.408 Round 3: 205 peptides, 33 chains. Longest chain 21 peptides. Score 0.471 Round 4: 205 peptides, 31 chains. Longest chain 25 peptides. Score 0.502 Round 5: 216 peptides, 34 chains. Longest chain 14 peptides. Score 0.495 Taking the results from Round 4 Chains 32, Residues 174, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 7089 restraints for refining 3019 atoms. 6384 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2608 (Rfree = 0.000) for 3019 atoms. Found 12 (14 requested) and removed 52 (7 requested) atoms. Cycle 2: After refmac, R = 0.2533 (Rfree = 0.000) for 2931 atoms. Found 9 (14 requested) and removed 32 (7 requested) atoms. Cycle 3: After refmac, R = 0.2370 (Rfree = 0.000) for 2874 atoms. Found 10 (13 requested) and removed 38 (6 requested) atoms. Cycle 4: After refmac, R = 0.2460 (Rfree = 0.000) for 2823 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 5: After refmac, R = 0.2379 (Rfree = 0.000) for 2798 atoms. Found 8 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.77 4.09 Search for helices and strands: 0 residues in 0 chains, 2909 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2928 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 11 peptides. Score 0.287 Round 2: 175 peptides, 33 chains. Longest chain 8 peptides. Score 0.357 Round 3: 182 peptides, 31 chains. Longest chain 14 peptides. Score 0.418 Round 4: 177 peptides, 32 chains. Longest chain 10 peptides. Score 0.382 Round 5: 194 peptides, 32 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 32, Residues 162, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6774 restraints for refining 2899 atoms. 6131 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2422 (Rfree = 0.000) for 2899 atoms. Found 10 (13 requested) and removed 58 (6 requested) atoms. Cycle 7: After refmac, R = 0.2088 (Rfree = 0.000) for 2824 atoms. Found 7 (13 requested) and removed 37 (6 requested) atoms. Cycle 8: After refmac, R = 0.1626 (Rfree = 0.000) for 2778 atoms. Found 2 (13 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 2756 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.2288 (Rfree = 0.000) for 2745 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.86 4.18 Search for helices and strands: 0 residues in 0 chains, 2830 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 2844 seeds are put forward Round 1: 149 peptides, 31 chains. Longest chain 8 peptides. Score 0.282 Round 2: 183 peptides, 32 chains. Longest chain 13 peptides. Score 0.405 Round 3: 180 peptides, 31 chains. Longest chain 11 peptides. Score 0.410 Round 4: 189 peptides, 32 chains. Longest chain 12 peptides. Score 0.428 Round 5: 197 peptides, 30 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 5 Chains 30, Residues 167, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6921 restraints for refining 3013 atoms. 6246 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2415 (Rfree = 0.000) for 3013 atoms. Found 14 (14 requested) and removed 44 (7 requested) atoms. Cycle 12: After refmac, R = 0.2244 (Rfree = 0.000) for 2949 atoms. Found 14 (14 requested) and removed 24 (7 requested) atoms. Cycle 13: After refmac, R = 0.2060 (Rfree = 0.000) for 2915 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 14: After refmac, R = 0.2009 (Rfree = 0.000) for 2876 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 15: After refmac, R = 0.1922 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 2989 seeds are put forward Round 1: 143 peptides, 32 chains. Longest chain 8 peptides. Score 0.237 Round 2: 161 peptides, 29 chains. Longest chain 13 peptides. Score 0.369 Round 3: 178 peptides, 32 chains. Longest chain 12 peptides. Score 0.386 Round 4: 177 peptides, 29 chains. Longest chain 13 peptides. Score 0.432 Round 5: 195 peptides, 35 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 4 Chains 29, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6926 restraints for refining 2925 atoms. 6363 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2044 (Rfree = 0.000) for 2925 atoms. Found 6 (13 requested) and removed 30 (6 requested) atoms. Cycle 17: After refmac, R = 0.2278 (Rfree = 0.000) for 2873 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.2014 (Rfree = 0.000) for 2852 atoms. Found 8 (13 requested) and removed 17 (6 requested) atoms. Cycle 19: After refmac, R = 0.1567 (Rfree = 0.000) for 2831 atoms. Found 3 (13 requested) and removed 13 (6 requested) atoms. Cycle 20: After refmac, R = 0.1375 (Rfree = 0.000) for 2810 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 2908 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2921 seeds are put forward Round 1: 117 peptides, 25 chains. Longest chain 9 peptides. Score 0.251 Round 2: 181 peptides, 31 chains. Longest chain 10 peptides. Score 0.414 Round 3: 184 peptides, 30 chains. Longest chain 11 peptides. Score 0.442 Round 4: 168 peptides, 27 chains. Longest chain 17 peptides. Score 0.431 Round 5: 161 peptides, 25 chains. Longest chain 18 peptides. Score 0.438 Taking the results from Round 3 Chains 30, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6420 restraints for refining 2845 atoms. 5834 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1982 (Rfree = 0.000) for 2845 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 22: After refmac, R = 0.1973 (Rfree = 0.000) for 2820 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 23: After refmac, R = 0.1826 (Rfree = 0.000) for 2802 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.2036 (Rfree = 0.000) for 2788 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.1793 (Rfree = 0.000) for 2772 atoms. Found 12 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 2895 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2909 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 8 peptides. Score 0.235 Round 2: 146 peptides, 26 chains. Longest chain 14 peptides. Score 0.360 Round 3: 150 peptides, 28 chains. Longest chain 13 peptides. Score 0.341 Round 4: 155 peptides, 26 chains. Longest chain 12 peptides. Score 0.397 Round 5: 146 peptides, 26 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 4 Chains 26, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6776 restraints for refining 2890 atoms. 6286 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2159 (Rfree = 0.000) for 2890 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 27: After refmac, R = 0.2169 (Rfree = 0.000) for 2857 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 28: After refmac, R = 0.2132 (Rfree = 0.000) for 2837 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 29: After refmac, R = 0.2107 (Rfree = 0.000) for 2819 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2067 (Rfree = 0.000) for 2807 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 2902 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2917 seeds are put forward Round 1: 118 peptides, 28 chains. Longest chain 6 peptides. Score 0.196 Round 2: 137 peptides, 28 chains. Longest chain 10 peptides. Score 0.285 Round 3: 131 peptides, 27 chains. Longest chain 8 peptides. Score 0.277 Round 4: 153 peptides, 29 chains. Longest chain 15 peptides. Score 0.336 Round 5: 158 peptides, 31 chains. Longest chain 8 peptides. Score 0.321 Taking the results from Round 4 Chains 29, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6750 restraints for refining 2883 atoms. 6283 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2243 (Rfree = 0.000) for 2883 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 32: After refmac, R = 0.2229 (Rfree = 0.000) for 2843 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 33: After refmac, R = 0.2138 (Rfree = 0.000) for 2816 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.2379 (Rfree = 0.000) for 2798 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 35: After refmac, R = 0.2097 (Rfree = 0.000) for 2785 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 4.07 Search for helices and strands: 0 residues in 0 chains, 2873 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2893 seeds are put forward Round 1: 92 peptides, 22 chains. Longest chain 6 peptides. Score 0.188 Round 2: 118 peptides, 24 chains. Longest chain 9 peptides. Score 0.275 Round 3: 130 peptides, 25 chains. Longest chain 9 peptides. Score 0.310 Round 4: 126 peptides, 24 chains. Longest chain 11 peptides. Score 0.311 Round 5: 139 peptides, 23 chains. Longest chain 18 peptides. Score 0.386 Taking the results from Round 5 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6330 restraints for refining 2773 atoms. 5889 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2270 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 37: After refmac, R = 0.2110 (Rfree = 0.000) for 2748 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.1991 (Rfree = 0.000) for 2735 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2128 (Rfree = 0.000) for 2726 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 40: After refmac, R = 0.1417 (Rfree = 0.000) for 2707 atoms. Found 5 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 4.12 Search for helices and strands: 0 residues in 0 chains, 2810 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2833 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 9 peptides. Score 0.225 Round 2: 119 peptides, 26 chains. Longest chain 8 peptides. Score 0.240 Round 3: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.284 Round 4: 122 peptides, 24 chains. Longest chain 10 peptides. Score 0.293 Round 5: 131 peptides, 24 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 5 Chains 24, Residues 107, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6154 restraints for refining 2693 atoms. 5750 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1908 (Rfree = 0.000) for 2693 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 42: After refmac, R = 0.1952 (Rfree = 0.000) for 2683 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 43: After refmac, R = 0.1981 (Rfree = 0.000) for 2669 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 44: After refmac, R = 0.1954 (Rfree = 0.000) for 2655 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 45: After refmac, R = 0.1858 (Rfree = 0.000) for 2652 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2730 seeds are put forward NCS extension: 0 residues added, 2730 seeds are put forward Round 1: 89 peptides, 21 chains. Longest chain 6 peptides. Score 0.194 Round 2: 105 peptides, 23 chains. Longest chain 7 peptides. Score 0.233 Round 3: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.305 Round 4: 121 peptides, 21 chains. Longest chain 14 peptides. Score 0.347 Round 5: 117 peptides, 20 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 97, 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 2fur-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3709 reflections ( 99.52 % complete ) and 6184 restraints for refining 2682 atoms. 5816 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2086 (Rfree = 0.000) for 2682 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2125 (Rfree = 0.000) for 2660 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2082 (Rfree = 0.000) for 2645 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2016 (Rfree = 0.000) for 2629 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:04:50 GMT 2018 Job finished. TimeTaking 38.63 Used memory is bytes: 7316216