Mon 24 Dec 00:22:05 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 2ogi-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ogi-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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/2ogi-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 00:22:09 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/2ogi-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ogi-3.4-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 289 and 0 Target number of residues in the AU: 289 Target solvent content: 0.6459 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.52 Input MTZ file: 2ogi-3.4-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: 65.860 52.534 70.037 90.000 114.298 90.000 Input sequence file: 2ogi-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.90 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: 63.833 3.400 Wilson plot Bfac: 75.24 6172 reflections ( 99.82 % complete ) and 0 restraints for refining 3465 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3009 (Rfree = 0.000) for 3465 atoms. Found 26 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.33 Search for helices and strands: 0 residues in 0 chains, 3565 seeds are put forward NCS extension: 0 residues added, 3565 seeds are put forward Round 1: 188 peptides, 39 chains. Longest chain 8 peptides. Score 0.298 Round 2: 209 peptides, 34 chains. Longest chain 13 peptides. Score 0.452 Round 3: 227 peptides, 34 chains. Longest chain 18 peptides. Score 0.511 Round 4: 235 peptides, 31 chains. Longest chain 20 peptides. Score 0.574 Round 5: 242 peptides, 33 chains. Longest chain 19 peptides. Score 0.569 Taking the results from Round 4 Chains 32, Residues 204, Estimated correctness of the model 20.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6020 restraints for refining 2850 atoms. 5133 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2737 (Rfree = 0.000) for 2850 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. Cycle 2: After refmac, R = 0.2480 (Rfree = 0.000) for 2794 atoms. Found 14 (21 requested) and removed 21 (10 requested) atoms. Cycle 3: After refmac, R = 0.2069 (Rfree = 0.000) for 2763 atoms. Found 11 (21 requested) and removed 17 (10 requested) atoms. Cycle 4: After refmac, R = 0.2270 (Rfree = 0.000) for 2739 atoms. Found 14 (20 requested) and removed 16 (10 requested) atoms. Cycle 5: After refmac, R = 0.2318 (Rfree = 0.000) for 2724 atoms. Found 16 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2862 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2881 seeds are put forward Round 1: 209 peptides, 37 chains. Longest chain 18 peptides. Score 0.408 Round 2: 221 peptides, 35 chains. Longest chain 15 peptides. Score 0.478 Round 3: 222 peptides, 31 chains. Longest chain 24 peptides. Score 0.536 Round 4: 226 peptides, 31 chains. Longest chain 20 peptides. Score 0.548 Round 5: 229 peptides, 30 chains. Longest chain 17 peptides. Score 0.570 Taking the results from Round 5 Chains 30, Residues 199, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6318 restraints for refining 2851 atoms. 5552 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2651 (Rfree = 0.000) for 2851 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 7: After refmac, R = 0.2506 (Rfree = 0.000) for 2805 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 8: After refmac, R = 0.2464 (Rfree = 0.000) for 2795 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 9: After refmac, R = 0.2510 (Rfree = 0.000) for 2788 atoms. Found 19 (21 requested) and removed 18 (10 requested) atoms. Cycle 10: After refmac, R = 0.2558 (Rfree = 0.000) for 2776 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.36 Search for helices and strands: 0 residues in 0 chains, 2924 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 2948 seeds are put forward Round 1: 182 peptides, 33 chains. Longest chain 17 peptides. Score 0.372 Round 2: 216 peptides, 35 chains. Longest chain 21 peptides. Score 0.461 Round 3: 211 peptides, 29 chains. Longest chain 22 peptides. Score 0.530 Round 4: 208 peptides, 33 chains. Longest chain 15 peptides. Score 0.463 Round 5: 230 peptides, 36 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 3 Chains 29, Residues 182, Estimated correctness of the model 4.2 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6195 restraints for refining 2810 atoms. 5451 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2584 (Rfree = 0.000) for 2810 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 12: After refmac, R = 0.2550 (Rfree = 0.000) for 2782 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2430 (Rfree = 0.000) for 2778 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 14: After refmac, R = 0.2505 (Rfree = 0.000) for 2775 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 15: After refmac, R = 0.2443 (Rfree = 0.000) for 2776 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.34 Search for helices and strands: 0 residues in 0 chains, 2900 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2922 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 10 peptides. Score 0.367 Round 2: 201 peptides, 31 chains. Longest chain 20 peptides. Score 0.469 Round 3: 207 peptides, 31 chains. Longest chain 13 peptides. Score 0.489 Round 4: 209 peptides, 30 chains. Longest chain 17 peptides. Score 0.510 Round 5: 227 peptides, 32 chains. Longest chain 20 peptides. Score 0.538 Taking the results from Round 5 Chains 32, Residues 195, Estimated correctness of the model 7.2 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6056 restraints for refining 2852 atoms. 5233 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2698 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 17: After refmac, R = 0.2615 (Rfree = 0.000) for 2833 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 18: After refmac, R = 0.2553 (Rfree = 0.000) for 2820 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 19: After refmac, R = 0.2525 (Rfree = 0.000) for 2810 atoms. Found 18 (21 requested) and removed 16 (10 requested) atoms. Cycle 20: After refmac, R = 0.2552 (Rfree = 0.000) for 2804 atoms. Found 20 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2934 seeds are put forward Round 1: 173 peptides, 33 chains. Longest chain 8 peptides. Score 0.337 Round 2: 187 peptides, 27 chains. Longest chain 17 peptides. Score 0.481 Round 3: 181 peptides, 28 chains. Longest chain 11 peptides. Score 0.446 Round 4: 186 peptides, 29 chains. Longest chain 11 peptides. Score 0.448 Round 5: 198 peptides, 27 chains. Longest chain 12 peptides. Score 0.517 Taking the results from Round 5 Chains 27, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6366 restraints for refining 2852 atoms. 5709 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2745 (Rfree = 0.000) for 2852 atoms. Found 19 (21 requested) and removed 17 (10 requested) atoms. Cycle 22: After refmac, R = 0.2711 (Rfree = 0.000) for 2837 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 23: After refmac, R = 0.2625 (Rfree = 0.000) for 2830 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 24: After refmac, R = 0.2498 (Rfree = 0.000) for 2825 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.2457 (Rfree = 0.000) for 2829 atoms. Found 21 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2949 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2963 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 11 peptides. Score 0.292 Round 2: 186 peptides, 32 chains. Longest chain 11 peptides. Score 0.402 Round 3: 178 peptides, 27 chains. Longest chain 12 peptides. Score 0.451 Round 4: 179 peptides, 28 chains. Longest chain 11 peptides. Score 0.439 Round 5: 177 peptides, 25 chains. Longest chain 16 peptides. Score 0.478 Taking the results from Round 5 Chains 25, Residues 152, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6247 restraints for refining 2852 atoms. 5620 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2592 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 24 (10 requested) atoms. Cycle 27: After refmac, R = 0.2538 (Rfree = 0.000) for 2833 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 28: After refmac, R = 0.2606 (Rfree = 0.000) for 2825 atoms. Found 16 (21 requested) and removed 15 (10 requested) atoms. Cycle 29: After refmac, R = 0.2574 (Rfree = 0.000) for 2816 atoms. Found 15 (21 requested) and removed 18 (10 requested) atoms. Cycle 30: After refmac, R = 0.2625 (Rfree = 0.000) for 2805 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.30 Search for helices and strands: 0 residues in 0 chains, 2922 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 2939 seeds are put forward Round 1: 140 peptides, 31 chains. Longest chain 7 peptides. Score 0.238 Round 2: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.376 Round 3: 161 peptides, 29 chains. Longest chain 10 peptides. Score 0.357 Round 4: 163 peptides, 27 chains. Longest chain 14 peptides. Score 0.397 Round 5: 166 peptides, 26 chains. Longest chain 11 peptides. Score 0.424 Taking the results from Round 5 Chains 26, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6378 restraints for refining 2852 atoms. 5844 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2798 (Rfree = 0.000) for 2852 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 32: After refmac, R = 0.2669 (Rfree = 0.000) for 2831 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 33: After refmac, R = 0.2670 (Rfree = 0.000) for 2822 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 34: After refmac, R = 0.2632 (Rfree = 0.000) for 2814 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 35: After refmac, R = 0.2553 (Rfree = 0.000) for 2815 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.28 Search for helices and strands: 0 residues in 0 chains, 2953 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2966 seeds are put forward Round 1: 122 peptides, 24 chains. Longest chain 11 peptides. Score 0.286 Round 2: 151 peptides, 29 chains. Longest chain 12 peptides. Score 0.318 Round 3: 160 peptides, 27 chains. Longest chain 12 peptides. Score 0.386 Round 4: 174 peptides, 29 chains. Longest chain 18 peptides. Score 0.406 Round 5: 166 peptides, 29 chains. Longest chain 19 peptides. Score 0.376 Taking the results from Round 4 Chains 29, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6072 restraints for refining 2774 atoms. 5521 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2563 (Rfree = 0.000) for 2774 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 37: After refmac, R = 0.2625 (Rfree = 0.000) for 2756 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 38: After refmac, R = 0.2654 (Rfree = 0.000) for 2743 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 39: After refmac, R = 0.2581 (Rfree = 0.000) for 2737 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 40: After refmac, R = 0.2544 (Rfree = 0.000) for 2735 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2845 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2865 seeds are put forward Round 1: 122 peptides, 26 chains. Longest chain 7 peptides. Score 0.250 Round 2: 161 peptides, 31 chains. Longest chain 11 peptides. Score 0.324 Round 3: 158 peptides, 30 chains. Longest chain 13 peptides. Score 0.329 Round 4: 152 peptides, 27 chains. Longest chain 12 peptides. Score 0.355 Round 5: 149 peptides, 25 chains. Longest chain 11 peptides. Score 0.377 Taking the results from Round 5 Chains 25, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6172 reflections ( 99.82 % complete ) and 6338 restraints for refining 2801 atoms. 5867 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2602 (Rfree = 0.000) for 2801 atoms. Found 21 (21 requested) and removed 35 (10 requested) atoms. Cycle 42: After refmac, R = 0.2740 (Rfree = 0.000) for 2778 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 43: After refmac, R = 0.2639 (Rfree = 0.000) for 2767 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.2706 (Rfree = 0.000) for 2765 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 45: After refmac, R = 0.2602 (Rfree = 0.000) for 2763 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.35 Search for helices and strands: 0 residues in 0 chains, 2884 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 2897 seeds are put forward Round 1: 97 peptides, 23 chains. Longest chain 6 peptides. Score 0.191 Round 2: 117 peptides, 23 chains. Longest chain 9 peptides. Score 0.283 Round 3: 122 peptides, 24 chains. Longest chain 8 peptides. Score 0.286 Round 4: 127 peptides, 24 chains. Longest chain 10 peptides. Score 0.307 Round 5: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 117, 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 2ogi-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6172 reflections ( 99.82 % complete ) and 5969 restraints for refining 2703 atoms. 5526 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2435 (Rfree = 0.000) for 2703 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2532 (Rfree = 0.000) for 2687 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2507 (Rfree = 0.000) for 2670 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2425 (Rfree = 0.000) for 2653 atoms. TimeTaking 32.72