null Mon 24 Dec 08:01:48 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fur-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fur-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-noncs ############### 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 08:01:53 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/noncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fur-4.0-parrot-noncs/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-noncs.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-noncs.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 = 0.3370 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3426 (Rfree = 0.000) for 3687 atoms. Found 17 (17 requested) and removed 468 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 0 residues added, 3249 seeds are put forward Round 1: 94 peptides, 21 chains. Longest chain 6 peptides. Score 0.220 Round 2: 135 peptides, 28 chains. Longest chain 8 peptides. Score 0.276 Round 3: 140 peptides, 27 chains. Longest chain 9 peptides. Score 0.317 Round 4: 135 peptides, 24 chains. Longest chain 10 peptides. Score 0.350 Round 5: 156 peptides, 28 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 5 Chains 28, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 7188 restraints for refining 3019 atoms. 6704 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3186 (Rfree = 0.000) for 3019 atoms. Found 14 (14 requested) and removed 105 (7 requested) atoms. Cycle 2: After refmac, R = 0.2983 (Rfree = 0.000) for 2897 atoms. Found 7 (13 requested) and removed 39 (6 requested) atoms. Cycle 3: After refmac, R = 0.2714 (Rfree = 0.000) for 2832 atoms. Found 0 (13 requested) and removed 46 (6 requested) atoms. Cycle 4: After refmac, R = 0.2521 (Rfree = 0.000) for 2771 atoms. Found 5 (13 requested) and removed 23 (6 requested) atoms. Cycle 5: After refmac, R = 0.2816 (Rfree = 0.000) for 2741 atoms. Found 2 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 4.01 Search for helices and strands: 0 residues in 0 chains, 2818 seeds are put forward NCS extension: 0 residues added, 2818 seeds are put forward Round 1: 125 peptides, 26 chains. Longest chain 9 peptides. Score 0.268 Round 2: 145 peptides, 27 chains. Longest chain 9 peptides. Score 0.338 Round 3: 152 peptides, 27 chains. Longest chain 9 peptides. Score 0.367 Round 4: 146 peptides, 25 chains. Longest chain 11 peptides. Score 0.378 Round 5: 159 peptides, 29 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 4 Chains 25, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6308 restraints for refining 2720 atoms. 5849 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2665 (Rfree = 0.000) for 2720 atoms. Found 5 (12 requested) and removed 27 (6 requested) atoms. Cycle 7: After refmac, R = 0.2474 (Rfree = 0.000) for 2678 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.2480 (Rfree = 0.000) for 2652 atoms. Found 12 (12 requested) and removed 42 (6 requested) atoms. Cycle 9: After refmac, R = 0.2275 (Rfree = 0.000) for 2615 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. Cycle 10: After refmac, R = 0.2482 (Rfree = 0.000) for 2599 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 2679 seeds are put forward NCS extension: 0 residues added, 2679 seeds are put forward Round 1: 131 peptides, 28 chains. Longest chain 7 peptides. Score 0.258 Round 2: 157 peptides, 28 chains. Longest chain 11 peptides. Score 0.370 Round 3: 164 peptides, 27 chains. Longest chain 13 peptides. Score 0.415 Round 4: 178 peptides, 28 chains. Longest chain 13 peptides. Score 0.452 Round 5: 162 peptides, 26 chains. Longest chain 22 peptides. Score 0.425 Taking the results from Round 4 Chains 28, Residues 150, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 5821 restraints for refining 2636 atoms. 5234 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2621 (Rfree = 0.000) for 2636 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 12: After refmac, R = 0.2390 (Rfree = 0.000) for 2601 atoms. Found 12 (12 requested) and removed 41 (6 requested) atoms. Cycle 13: After refmac, R = 0.2205 (Rfree = 0.000) for 2558 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 14: After refmac, R = 0.2176 (Rfree = 0.000) for 2545 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 15: After refmac, R = 0.2104 (Rfree = 0.000) for 2533 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 2628 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 2642 seeds are put forward Round 1: 121 peptides, 27 chains. Longest chain 6 peptides. Score 0.230 Round 2: 165 peptides, 28 chains. Longest chain 12 peptides. Score 0.402 Round 3: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.412 Round 4: 153 peptides, 25 chains. Longest chain 12 peptides. Score 0.407 Round 5: 155 peptides, 23 chains. Longest chain 17 peptides. Score 0.449 Taking the results from Round 5 Chains 23, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6511 restraints for refining 2798 atoms. 6006 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2150 (Rfree = 0.000) for 2798 atoms. Found 6 (13 requested) and removed 32 (6 requested) atoms. Cycle 17: After refmac, R = 0.2371 (Rfree = 0.000) for 2754 atoms. Found 12 (13 requested) and removed 19 (6 requested) atoms. Cycle 18: After refmac, R = 0.2389 (Rfree = 0.000) for 2727 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 19: After refmac, R = 0.2380 (Rfree = 0.000) for 2713 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 20: After refmac, R = 0.2294 (Rfree = 0.000) for 2700 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2831 seeds are put forward Round 1: 126 peptides, 26 chains. Longest chain 8 peptides. Score 0.273 Round 2: 145 peptides, 28 chains. Longest chain 10 peptides. Score 0.320 Round 3: 152 peptides, 26 chains. Longest chain 12 peptides. Score 0.385 Round 4: 138 peptides, 24 chains. Longest chain 12 peptides. Score 0.363 Round 5: 138 peptides, 24 chains. Longest chain 13 peptides. Score 0.363 Taking the results from Round 3 Chains 26, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6533 restraints for refining 2773 atoms. 6055 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2276 (Rfree = 0.000) for 2773 atoms. Found 9 (13 requested) and removed 22 (6 requested) atoms. Cycle 22: After refmac, R = 0.2210 (Rfree = 0.000) for 2749 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.2076 (Rfree = 0.000) for 2734 atoms. Found 10 (13 requested) and removed 15 (6 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 2718 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 25: After refmac, R = 0.1982 (Rfree = 0.000) for 2703 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 4.10 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 0 residues added, 2809 seeds are put forward Round 1: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.231 Round 2: 111 peptides, 22 chains. Longest chain 12 peptides. Score 0.282 Round 3: 122 peptides, 22 chains. Longest chain 9 peptides. Score 0.332 Round 4: 120 peptides, 22 chains. Longest chain 10 peptides. Score 0.323 Round 5: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.332 Taking the results from Round 5 Chains 22, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6531 restraints for refining 2767 atoms. 6153 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2099 (Rfree = 0.000) for 2767 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 27: After refmac, R = 0.2248 (Rfree = 0.000) for 2749 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.2056 (Rfree = 0.000) for 2732 atoms. Found 13 (13 requested) and removed 32 (6 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 2705 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 30: After refmac, R = 0.2010 (Rfree = 0.000) for 2696 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.89 4.22 Search for helices and strands: 0 residues in 0 chains, 2780 seeds are put forward NCS extension: 0 residues added, 2780 seeds are put forward Round 1: 101 peptides, 24 chains. Longest chain 5 peptides. Score 0.193 Round 2: 114 peptides, 23 chains. Longest chain 7 peptides. Score 0.276 Round 3: 116 peptides, 22 chains. Longest chain 9 peptides. Score 0.305 Round 4: 118 peptides, 21 chains. Longest chain 12 peptides. Score 0.333 Round 5: 122 peptides, 24 chains. Longest chain 8 peptides. Score 0.293 Taking the results from Round 4 Chains 21, Residues 97, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6233 restraints for refining 2700 atoms. 5866 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2332 (Rfree = 0.000) for 2700 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 2666 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2176 (Rfree = 0.000) for 2654 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.2008 (Rfree = 0.000) for 2648 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.2197 (Rfree = 0.000) for 2650 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 2744 seeds are put forward NCS extension: 0 residues added, 2744 seeds are put forward Round 1: 105 peptides, 24 chains. Longest chain 6 peptides. Score 0.213 Round 2: 116 peptides, 23 chains. Longest chain 7 peptides. Score 0.285 Round 3: 118 peptides, 22 chains. Longest chain 11 peptides. Score 0.314 Round 4: 122 peptides, 22 chains. Longest chain 7 peptides. Score 0.332 Round 5: 132 peptides, 23 chains. Longest chain 10 peptides. Score 0.356 Taking the results from Round 5 Chains 23, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6503 restraints for refining 2759 atoms. 6090 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2119 (Rfree = 0.000) for 2759 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 37: After refmac, R = 0.2087 (Rfree = 0.000) for 2734 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 38: After refmac, R = 0.2139 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1981 (Rfree = 0.000) for 2704 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 40: After refmac, R = 0.2180 (Rfree = 0.000) for 2697 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.89 4.22 Search for helices and strands: 0 residues in 0 chains, 2756 seeds are put forward NCS extension: 0 residues added, 2756 seeds are put forward Round 1: 88 peptides, 21 chains. Longest chain 6 peptides. Score 0.188 Round 2: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.286 Round 3: 90 peptides, 19 chains. Longest chain 7 peptides. Score 0.242 Round 4: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.272 Round 5: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.253 Taking the results from Round 2 Chains 19, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6215 restraints for refining 2664 atoms. 5914 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2198 (Rfree = 0.000) for 2664 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 42: After refmac, R = 0.2310 (Rfree = 0.000) for 2646 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 43: After refmac, R = 0.2280 (Rfree = 0.000) for 2635 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2221 (Rfree = 0.000) for 2627 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 45: After refmac, R = 0.1957 (Rfree = 0.000) for 2619 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 2692 seeds are put forward NCS extension: 0 residues added, 2692 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 6 peptides. Score 0.205 Round 2: 102 peptides, 21 chains. Longest chain 8 peptides. Score 0.259 Round 3: 104 peptides, 20 chains. Longest chain 8 peptides. Score 0.289 Round 4: 96 peptides, 19 chains. Longest chain 8 peptides. Score 0.272 Round 5: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.280 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 84, 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 5930 restraints for refining 2617 atoms. 5614 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2139 (Rfree = 0.000) for 2617 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2052 (Rfree = 0.000) for 2594 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2298 (Rfree = 0.000) for 2577 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2218 (Rfree = 0.000) for 2569 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:33:23 GMT 2018 Job finished. TimeTaking 31.58 Used memory is bytes: 21213352