Sun 23 Dec 23:56:44 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 2fqp-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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/2fqp-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 ============================================================ Sun 23 Dec 23:56:49 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/2fqp-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.2-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 252 and 0 Target number of residues in the AU: 252 Target solvent content: 0.5972 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.2-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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 3.200 Wilson plot Bfac: 51.11 4635 reflections ( 83.48 % complete ) and 0 restraints for refining 3415 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3117 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2329 (Rfree = 0.000) for 3415 atoms. Found 23 (30 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.95 3.47 Search for helices and strands: 0 residues in 0 chains, 3419 seeds are put forward NCS extension: 0 residues added, 3419 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 8 peptides. Score 0.268 Round 2: 155 peptides, 29 chains. Longest chain 10 peptides. Score 0.370 Round 3: 173 peptides, 31 chains. Longest chain 10 peptides. Score 0.415 Round 4: 174 peptides, 28 chains. Longest chain 16 peptides. Score 0.476 Round 5: 160 peptides, 24 chains. Longest chain 13 peptides. Score 0.490 Taking the results from Round 5 Chains 24, Residues 136, Estimated correctness of the model 8.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6578 restraints for refining 2834 atoms. 6058 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2077 (Rfree = 0.000) for 2834 atoms. Found 17 (25 requested) and removed 16 (12 requested) atoms. Cycle 2: After refmac, R = 0.1889 (Rfree = 0.000) for 2815 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. Cycle 3: After refmac, R = 0.1890 (Rfree = 0.000) for 2805 atoms. Found 4 (25 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.1863 (Rfree = 0.000) for 2791 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 5: After refmac, R = 0.1818 (Rfree = 0.000) for 2778 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 3.43 Search for helices and strands: 0 residues in 0 chains, 2804 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 2819 seeds are put forward Round 1: 166 peptides, 26 chains. Longest chain 14 peptides. Score 0.479 Round 2: 188 peptides, 28 chains. Longest chain 14 peptides. Score 0.533 Round 3: 197 peptides, 30 chains. Longest chain 14 peptides. Score 0.534 Round 4: 180 peptides, 24 chains. Longest chain 17 peptides. Score 0.570 Round 5: 182 peptides, 26 chains. Longest chain 14 peptides. Score 0.544 Taking the results from Round 4 Chains 25, Residues 156, Estimated correctness of the model 32.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6321 restraints for refining 2793 atoms. 5679 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2013 (Rfree = 0.000) for 2793 atoms. Found 22 (25 requested) and removed 14 (12 requested) atoms. Cycle 7: After refmac, R = 0.1788 (Rfree = 0.000) for 2791 atoms. Found 9 (25 requested) and removed 12 (12 requested) atoms. Cycle 8: After refmac, R = 0.1864 (Rfree = 0.000) for 2778 atoms. Found 9 (25 requested) and removed 13 (12 requested) atoms. Cycle 9: After refmac, R = 0.1843 (Rfree = 0.000) for 2765 atoms. Found 9 (24 requested) and removed 14 (12 requested) atoms. Cycle 10: After refmac, R = 0.1874 (Rfree = 0.000) for 2754 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 3.40 Search for helices and strands: 0 residues in 0 chains, 2793 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2808 seeds are put forward Round 1: 179 peptides, 28 chains. Longest chain 13 peptides. Score 0.497 Round 2: 193 peptides, 27 chains. Longest chain 17 peptides. Score 0.569 Round 3: 196 peptides, 26 chains. Longest chain 14 peptides. Score 0.595 Round 4: 193 peptides, 27 chains. Longest chain 13 peptides. Score 0.569 Round 5: 189 peptides, 29 chains. Longest chain 15 peptides. Score 0.520 Taking the results from Round 3 Chains 26, Residues 170, Estimated correctness of the model 39.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6229 restraints for refining 2775 atoms. 5575 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2006 (Rfree = 0.000) for 2775 atoms. Found 16 (24 requested) and removed 18 (12 requested) atoms. Cycle 12: After refmac, R = 0.1680 (Rfree = 0.000) for 2763 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. Cycle 13: After refmac, R = 0.1637 (Rfree = 0.000) for 2747 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 14: After refmac, R = 0.1536 (Rfree = 0.000) for 2739 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.1537 (Rfree = 0.000) for 2726 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.91 3.43 Search for helices and strands: 0 residues in 0 chains, 2758 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2770 seeds are put forward Round 1: 170 peptides, 28 chains. Longest chain 13 peptides. Score 0.459 Round 2: 190 peptides, 29 chains. Longest chain 14 peptides. Score 0.524 Round 3: 196 peptides, 25 chains. Longest chain 15 peptides. Score 0.611 Round 4: 197 peptides, 27 chains. Longest chain 17 peptides. Score 0.583 Round 5: 196 peptides, 29 chains. Longest chain 14 peptides. Score 0.547 Taking the results from Round 3 Chains 26, Residues 171, Estimated correctness of the model 44.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 5952 restraints for refining 2743 atoms. 5251 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1829 (Rfree = 0.000) for 2743 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 17: After refmac, R = 0.1687 (Rfree = 0.000) for 2730 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. Cycle 18: After refmac, R = 0.1616 (Rfree = 0.000) for 2715 atoms. Found 7 (24 requested) and removed 13 (12 requested) atoms. Cycle 19: After refmac, R = 0.1526 (Rfree = 0.000) for 2702 atoms. Found 12 (24 requested) and removed 13 (12 requested) atoms. Cycle 20: After refmac, R = 0.1555 (Rfree = 0.000) for 2693 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 3.40 Search for helices and strands: 0 residues in 0 chains, 2760 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2775 seeds are put forward Round 1: 162 peptides, 26 chains. Longest chain 17 peptides. Score 0.461 Round 2: 184 peptides, 28 chains. Longest chain 12 peptides. Score 0.517 Round 3: 185 peptides, 26 chains. Longest chain 17 peptides. Score 0.555 Round 4: 173 peptides, 28 chains. Longest chain 17 peptides. Score 0.471 Round 5: 190 peptides, 27 chains. Longest chain 13 peptides. Score 0.557 Taking the results from Round 5 Chains 27, Residues 163, Estimated correctness of the model 28.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6159 restraints for refining 2723 atoms. 5534 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1895 (Rfree = 0.000) for 2723 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. Cycle 22: After refmac, R = 0.1810 (Rfree = 0.000) for 2708 atoms. Found 5 (24 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.1759 (Rfree = 0.000) for 2697 atoms. Found 11 (24 requested) and removed 12 (12 requested) atoms. Cycle 24: After refmac, R = 0.1695 (Rfree = 0.000) for 2691 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.1702 (Rfree = 0.000) for 2676 atoms. Found 6 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.88 3.39 Search for helices and strands: 0 residues in 0 chains, 2732 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2744 seeds are put forward Round 1: 172 peptides, 29 chains. Longest chain 10 peptides. Score 0.448 Round 2: 192 peptides, 26 chains. Longest chain 14 peptides. Score 0.581 Round 3: 188 peptides, 30 chains. Longest chain 13 peptides. Score 0.498 Round 4: 193 peptides, 29 chains. Longest chain 12 peptides. Score 0.535 Round 5: 180 peptides, 27 chains. Longest chain 14 peptides. Score 0.519 Taking the results from Round 2 Chains 26, Residues 166, Estimated correctness of the model 35.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 5862 restraints for refining 2678 atoms. 5224 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1769 (Rfree = 0.000) for 2678 atoms. Found 12 (24 requested) and removed 17 (12 requested) atoms. Cycle 27: After refmac, R = 0.1749 (Rfree = 0.000) for 2670 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.1608 (Rfree = 0.000) for 2666 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1552 (Rfree = 0.000) for 2655 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1491 (Rfree = 0.000) for 2647 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.88 3.39 Search for helices and strands: 0 residues in 0 chains, 2682 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2697 seeds are put forward Round 1: 147 peptides, 23 chains. Longest chain 11 peptides. Score 0.453 Round 2: 163 peptides, 22 chains. Longest chain 14 peptides. Score 0.539 Round 3: 169 peptides, 21 chains. Longest chain 16 peptides. Score 0.579 Round 4: 170 peptides, 23 chains. Longest chain 14 peptides. Score 0.549 Round 5: 165 peptides, 24 chains. Longest chain 13 peptides. Score 0.511 Taking the results from Round 3 Chains 21, Residues 148, Estimated correctness of the model 35.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6092 restraints for refining 2706 atoms. 5521 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1804 (Rfree = 0.000) for 2706 atoms. Found 3 (24 requested) and removed 15 (12 requested) atoms. Cycle 32: After refmac, R = 0.1748 (Rfree = 0.000) for 2692 atoms. Found 14 (24 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.1575 (Rfree = 0.000) for 2686 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. Cycle 34: After refmac, R = 0.1507 (Rfree = 0.000) for 2677 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.1564 (Rfree = 0.000) for 2666 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.86 3.37 Search for helices and strands: 0 residues in 0 chains, 2707 seeds are put forward NCS extension: 0 residues added, 2707 seeds are put forward Round 1: 157 peptides, 24 chains. Longest chain 17 peptides. Score 0.477 Round 2: 153 peptides, 21 chains. Longest chain 19 peptides. Score 0.517 Round 3: 158 peptides, 25 chains. Longest chain 12 peptides. Score 0.463 Round 4: 172 peptides, 27 chains. Longest chain 11 peptides. Score 0.486 Round 5: 172 peptides, 24 chains. Longest chain 23 peptides. Score 0.539 Taking the results from Round 5 Chains 24, Residues 148, Estimated correctness of the model 23.6 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6038 restraints for refining 2726 atoms. 5436 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1921 (Rfree = 0.000) for 2726 atoms. Found 14 (24 requested) and removed 17 (12 requested) atoms. Cycle 37: After refmac, R = 0.1804 (Rfree = 0.000) for 2715 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. Cycle 38: After refmac, R = 0.2076 (Rfree = 0.000) for 2710 atoms. Found 24 (24 requested) and removed 13 (12 requested) atoms. Cycle 39: After refmac, R = 0.2133 (Rfree = 0.000) for 2719 atoms. Found 23 (24 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.1902 (Rfree = 0.000) for 2725 atoms. Found 15 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.85 3.35 Search for helices and strands: 0 residues in 0 chains, 2772 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 2803 seeds are put forward Round 1: 156 peptides, 27 chains. Longest chain 13 peptides. Score 0.415 Round 2: 180 peptides, 27 chains. Longest chain 14 peptides. Score 0.519 Round 3: 169 peptides, 24 chains. Longest chain 15 peptides. Score 0.527 Round 4: 169 peptides, 24 chains. Longest chain 12 peptides. Score 0.527 Round 5: 167 peptides, 25 chains. Longest chain 12 peptides. Score 0.501 Taking the results from Round 4 Chains 24, Residues 145, Estimated correctness of the model 19.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4635 reflections ( 83.48 % complete ) and 6092 restraints for refining 2713 atoms. 5536 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1872 (Rfree = 0.000) for 2713 atoms. Found 17 (24 requested) and removed 12 (12 requested) atoms. Cycle 42: After refmac, R = 0.1769 (Rfree = 0.000) for 2717 atoms. Found 15 (24 requested) and removed 12 (12 requested) atoms. Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 2718 atoms. Found 13 (24 requested) and removed 13 (12 requested) atoms. Cycle 44: After refmac, R = 0.1630 (Rfree = 0.000) for 2716 atoms. Found 10 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.1657 (Rfree = 0.000) for 2709 atoms. Found 9 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.41 Search for helices and strands: 0 residues in 0 chains, 2755 seeds are put forward NCS extension: 0 residues added, 2755 seeds are put forward Round 1: 144 peptides, 26 chains. Longest chain 10 peptides. Score 0.379 Round 2: 160 peptides, 25 chains. Longest chain 13 peptides. Score 0.471 Round 3: 158 peptides, 24 chains. Longest chain 12 peptides. Score 0.482 Round 4: 167 peptides, 25 chains. Longest chain 14 peptides. Score 0.501 Round 5: 149 peptides, 23 chains. Longest chain 14 peptides. Score 0.462 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 142, Estimated correctness of the model 11.7 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4635 reflections ( 83.48 % complete ) and 6010 restraints for refining 2692 atoms. 5467 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1800 (Rfree = 0.000) for 2692 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1784 (Rfree = 0.000) for 2676 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1783 (Rfree = 0.000) for 2662 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1761 (Rfree = 0.000) for 2651 atoms. TimeTaking 29.75