Mon 24 Dec 07:51:15 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 2p97-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p97-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p97-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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/2p97-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 07:51:20 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/2p97-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p97-4.0-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 327 and 0 Target number of residues in the AU: 327 Target solvent content: 0.6536 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-4.0-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3216 target number of atoms Had to go as low as 0.85 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: 72.889 4.001 Wilson plot Bfac: 80.39 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4698 reflections ( 99.62 % complete ) and 0 restraints for refining 3540 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3443 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3273 (Rfree = 0.000) for 3540 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 3611 seeds are put forward NCS extension: 0 residues added, 3611 seeds are put forward Round 1: 187 peptides, 37 chains. Longest chain 10 peptides. Score 0.310 Round 2: 239 peptides, 31 chains. Longest chain 20 peptides. Score 0.547 Round 3: 256 peptides, 27 chains. Longest chain 25 peptides. Score 0.632 Round 4: 270 peptides, 31 chains. Longest chain 19 peptides. Score 0.622 Round 5: 265 peptides, 31 chains. Longest chain 23 peptides. Score 0.610 Taking the results from Round 3 Chains 29, Residues 229, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6567 restraints for refining 2901 atoms. 5644 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2659 (Rfree = 0.000) for 2901 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 2: After refmac, R = 0.2607 (Rfree = 0.000) for 2846 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2501 (Rfree = 0.000) for 2819 atoms. Found 11 (13 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.2419 (Rfree = 0.000) for 2803 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2359 (Rfree = 0.000) for 2799 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.74 3.40 Search for helices and strands: 0 residues in 0 chains, 2888 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2903 seeds are put forward Round 1: 207 peptides, 30 chains. Longest chain 13 peptides. Score 0.471 Round 2: 234 peptides, 32 chains. Longest chain 15 peptides. Score 0.521 Round 3: 240 peptides, 27 chains. Longest chain 19 peptides. Score 0.595 Round 4: 239 peptides, 27 chains. Longest chain 19 peptides. Score 0.593 Round 5: 258 peptides, 29 chains. Longest chain 21 peptides. Score 0.615 Taking the results from Round 5 Chains 29, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6599 restraints for refining 2904 atoms. 5712 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2531 (Rfree = 0.000) for 2904 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 7: After refmac, R = 0.2308 (Rfree = 0.000) for 2889 atoms. Found 6 (13 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.2376 (Rfree = 0.000) for 2873 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 9: After refmac, R = 0.2290 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 10: After refmac, R = 0.2067 (Rfree = 0.000) for 2853 atoms. Found 4 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2955 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 2976 seeds are put forward Round 1: 217 peptides, 34 chains. Longest chain 12 peptides. Score 0.448 Round 2: 242 peptides, 33 chains. Longest chain 20 peptides. Score 0.531 Round 3: 225 peptides, 28 chains. Longest chain 19 peptides. Score 0.546 Round 4: 232 peptides, 27 chains. Longest chain 22 peptides. Score 0.575 Round 5: 248 peptides, 29 chains. Longest chain 21 peptides. Score 0.592 Taking the results from Round 5 Chains 29, Residues 219, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6583 restraints for refining 2904 atoms. 5736 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2276 (Rfree = 0.000) for 2904 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.2042 (Rfree = 0.000) for 2872 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2132 (Rfree = 0.000) for 2854 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1988 (Rfree = 0.000) for 2847 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.2018 (Rfree = 0.000) for 2831 atoms. Found 9 (13 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2916 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 2938 seeds are put forward Round 1: 200 peptides, 34 chains. Longest chain 13 peptides. Score 0.395 Round 2: 235 peptides, 34 chains. Longest chain 16 peptides. Score 0.500 Round 3: 227 peptides, 33 chains. Longest chain 19 peptides. Score 0.490 Round 4: 236 peptides, 32 chains. Longest chain 16 peptides. Score 0.527 Round 5: 232 peptides, 33 chains. Longest chain 17 peptides. Score 0.504 Taking the results from Round 4 Chains 32, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6695 restraints for refining 2904 atoms. 5911 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2292 (Rfree = 0.000) for 2904 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 17: After refmac, R = 0.2184 (Rfree = 0.000) for 2892 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 18: After refmac, R = 0.2160 (Rfree = 0.000) for 2884 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.2138 (Rfree = 0.000) for 2868 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 2855 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.30 Search for helices and strands: 0 residues in 0 chains, 2953 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2979 seeds are put forward Round 1: 190 peptides, 33 chains. Longest chain 15 peptides. Score 0.377 Round 2: 191 peptides, 31 chains. Longest chain 14 peptides. Score 0.408 Round 3: 201 peptides, 32 chains. Longest chain 14 peptides. Score 0.426 Round 4: 207 peptides, 30 chains. Longest chain 13 peptides. Score 0.471 Round 5: 219 peptides, 31 chains. Longest chain 19 peptides. Score 0.492 Taking the results from Round 5 Chains 31, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6858 restraints for refining 2904 atoms. 6137 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2237 (Rfree = 0.000) for 2904 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2061 (Rfree = 0.000) for 2888 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2016 (Rfree = 0.000) for 2879 atoms. Found 2 (13 requested) and removed 6 (6 requested) atoms. Cycle 24: After refmac, R = 0.1991 (Rfree = 0.000) for 2872 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.1970 (Rfree = 0.000) for 2868 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2927 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 2949 seeds are put forward Round 1: 201 peptides, 40 chains. Longest chain 12 peptides. Score 0.315 Round 2: 220 peptides, 33 chains. Longest chain 17 peptides. Score 0.470 Round 3: 226 peptides, 35 chains. Longest chain 15 peptides. Score 0.462 Round 4: 219 peptides, 31 chains. Longest chain 15 peptides. Score 0.492 Round 5: 226 peptides, 32 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 5 Chains 32, Residues 194, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6732 restraints for refining 2904 atoms. 5942 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2197 (Rfree = 0.000) for 2904 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2037 (Rfree = 0.000) for 2879 atoms. Found 2 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1966 (Rfree = 0.000) for 2853 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.1910 (Rfree = 0.000) for 2839 atoms. Found 4 (13 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1968 (Rfree = 0.000) for 2832 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 2911 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 2932 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 13 peptides. Score 0.288 Round 2: 214 peptides, 35 chains. Longest chain 14 peptides. Score 0.426 Round 3: 213 peptides, 31 chains. Longest chain 17 peptides. Score 0.475 Round 4: 188 peptides, 27 chains. Longest chain 15 peptides. Score 0.454 Round 5: 199 peptides, 27 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 5 Chains 27, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6881 restraints for refining 2904 atoms. 6220 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2074 (Rfree = 0.000) for 2904 atoms. Found 4 (13 requested) and removed 12 (6 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 2884 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.1899 (Rfree = 0.000) for 2873 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 34: After refmac, R = 0.1893 (Rfree = 0.000) for 2866 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1873 (Rfree = 0.000) for 2862 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.37 Search for helices and strands: 0 residues in 0 chains, 2939 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2953 seeds are put forward Round 1: 176 peptides, 35 chains. Longest chain 9 peptides. Score 0.301 Round 2: 206 peptides, 35 chains. Longest chain 20 peptides. Score 0.401 Round 3: 215 peptides, 33 chains. Longest chain 15 peptides. Score 0.455 Round 4: 219 peptides, 30 chains. Longest chain 15 peptides. Score 0.505 Round 5: 220 peptides, 32 chains. Longest chain 16 peptides. Score 0.482 Taking the results from Round 4 Chains 30, Residues 189, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6724 restraints for refining 2904 atoms. 5998 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2249 (Rfree = 0.000) for 2904 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2242 (Rfree = 0.000) for 2893 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. Cycle 38: After refmac, R = 0.2126 (Rfree = 0.000) for 2885 atoms. Found 2 (13 requested) and removed 9 (6 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2152 (Rfree = 0.000) for 2877 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2170 (Rfree = 0.000) for 2872 atoms. Found 3 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.40 Search for helices and strands: 0 residues in 0 chains, 2969 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2987 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 15 peptides. Score 0.346 Round 2: 192 peptides, 29 chains. Longest chain 19 peptides. Score 0.439 Round 3: 202 peptides, 33 chains. Longest chain 19 peptides. Score 0.415 Round 4: 199 peptides, 33 chains. Longest chain 16 peptides. Score 0.406 Round 5: 204 peptides, 30 chains. Longest chain 20 peptides. Score 0.462 Taking the results from Round 5 Chains 30, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4698 reflections ( 99.62 % complete ) and 6869 restraints for refining 2904 atoms. 6203 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2328 (Rfree = 0.000) for 2904 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.2133 (Rfree = 0.000) for 2887 atoms. Found 1 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2080 (Rfree = 0.000) for 2877 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1955 (Rfree = 0.000) for 2864 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.1955 (Rfree = 0.000) for 2849 atoms. Found 1 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 3.35 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2938 seeds are put forward Round 1: 147 peptides, 31 chains. Longest chain 11 peptides. Score 0.257 Round 2: 185 peptides, 32 chains. Longest chain 18 peptides. Score 0.375 Round 3: 187 peptides, 32 chains. Longest chain 19 peptides. Score 0.382 Round 4: 183 peptides, 29 chains. Longest chain 19 peptides. Score 0.411 Round 5: 177 peptides, 27 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 150, 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 2p97-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4698 reflections ( 99.62 % complete ) and 7151 restraints for refining 2903 atoms. 6578 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2070 (Rfree = 0.000) for 2903 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1944 (Rfree = 0.000) for 2888 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2003 (Rfree = 0.000) for 2874 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1794 (Rfree = 0.000) for 2862 atoms. TimeTaking 35.67