null Mon 24 Dec 07:27:24 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 1zkg-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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/1zkg-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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 07:27:28 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/1zkg-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.2-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 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.6389 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 424 Adjusted target solvent content: 0.53 Input MTZ file: 1zkg-3.2-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: 4 Cell parameters: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 3392 target number of atoms Had to go as low as 0.75 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: 29.148 3.200 Wilson plot Bfac: 71.17 7991 reflections ( 99.85 % complete ) and 0 restraints for refining 3738 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3349 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3014 (Rfree = 0.000) for 3738 atoms. Found 33 (33 requested) and removed 37 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.19 Search for helices and strands: 0 residues in 0 chains, 3864 seeds are put forward NCS extension: 0 residues added, 3864 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.309 Round 2: 245 peptides, 42 chains. Longest chain 11 peptides. Score 0.437 Round 3: 266 peptides, 39 chains. Longest chain 15 peptides. Score 0.536 Round 4: 251 peptides, 31 chains. Longest chain 21 peptides. Score 0.590 Round 5: 252 peptides, 32 chains. Longest chain 20 peptides. Score 0.581 Taking the results from Round 4 Chains 31, Residues 220, Estimated correctness of the model 38.3 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6728 restraints for refining 3094 atoms. 5782 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2624 (Rfree = 0.000) for 3094 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Cycle 2: After refmac, R = 0.2428 (Rfree = 0.000) for 3057 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2410 (Rfree = 0.000) for 3045 atoms. Found 23 (27 requested) and removed 18 (13 requested) atoms. Cycle 4: After refmac, R = 0.2371 (Rfree = 0.000) for 3035 atoms. Found 15 (27 requested) and removed 20 (13 requested) atoms. Cycle 5: After refmac, R = 0.2310 (Rfree = 0.000) for 3023 atoms. Found 18 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 3193 seeds are put forward NCS extension: 0 residues added, 3193 seeds are put forward Round 1: 219 peptides, 36 chains. Longest chain 15 peptides. Score 0.437 Round 2: 245 peptides, 34 chains. Longest chain 19 peptides. Score 0.539 Round 3: 247 peptides, 33 chains. Longest chain 16 peptides. Score 0.556 Round 4: 265 peptides, 32 chains. Longest chain 17 peptides. Score 0.613 Round 5: 237 peptides, 32 chains. Longest chain 15 peptides. Score 0.541 Taking the results from Round 4 Chains 34, Residues 233, Estimated correctness of the model 44.5 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6698 restraints for refining 3096 atoms. 5698 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 3096 atoms. Found 23 (27 requested) and removed 26 (13 requested) atoms. Cycle 7: After refmac, R = 0.2446 (Rfree = 0.000) for 3063 atoms. Found 21 (27 requested) and removed 28 (13 requested) atoms. Cycle 8: After refmac, R = 0.2317 (Rfree = 0.000) for 3041 atoms. Found 16 (27 requested) and removed 27 (13 requested) atoms. Cycle 9: After refmac, R = 0.2830 (Rfree = 0.000) for 3024 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 10: After refmac, R = 0.2524 (Rfree = 0.000) for 2997 atoms. Found 27 (27 requested) and removed 44 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 3152 seeds are put forward NCS extension: 7 residues added (1 deleted due to clashes), 3159 seeds are put forward Round 1: 193 peptides, 35 chains. Longest chain 14 peptides. Score 0.366 Round 2: 230 peptides, 33 chains. Longest chain 14 peptides. Score 0.509 Round 3: 241 peptides, 36 chains. Longest chain 14 peptides. Score 0.503 Round 4: 246 peptides, 35 chains. Longest chain 14 peptides. Score 0.530 Round 5: 252 peptides, 35 chains. Longest chain 17 peptides. Score 0.546 Taking the results from Round 5 Chains 35, Residues 217, Estimated correctness of the model 25.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6906 restraints for refining 3095 atoms. 6031 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2557 (Rfree = 0.000) for 3095 atoms. Found 26 (27 requested) and removed 29 (13 requested) atoms. Cycle 12: After refmac, R = 0.2411 (Rfree = 0.000) for 3078 atoms. Found 9 (27 requested) and removed 19 (13 requested) atoms. Cycle 13: After refmac, R = 0.2767 (Rfree = 0.000) for 3057 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 14: After refmac, R = 0.2361 (Rfree = 0.000) for 3046 atoms. Found 20 (27 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.2229 (Rfree = 0.000) for 3037 atoms. Found 19 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 3199 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3230 seeds are put forward Round 1: 208 peptides, 40 chains. Longest chain 9 peptides. Score 0.344 Round 2: 236 peptides, 35 chains. Longest chain 12 peptides. Score 0.501 Round 3: 226 peptides, 31 chains. Longest chain 19 peptides. Score 0.523 Round 4: 234 peptides, 33 chains. Longest chain 21 peptides. Score 0.521 Round 5: 239 peptides, 32 chains. Longest chain 22 peptides. Score 0.547 Taking the results from Round 5 Chains 34, Residues 207, Estimated correctness of the model 26.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6704 restraints for refining 3096 atoms. 5842 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2356 (Rfree = 0.000) for 3096 atoms. Found 22 (27 requested) and removed 17 (13 requested) atoms. Cycle 17: After refmac, R = 0.2242 (Rfree = 0.000) for 3090 atoms. Found 10 (27 requested) and removed 21 (13 requested) atoms. Cycle 18: After refmac, R = 0.2638 (Rfree = 0.000) for 3077 atoms. Found 27 (27 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2517 (Rfree = 0.000) for 3079 atoms. Found 26 (27 requested) and removed 23 (13 requested) atoms. Cycle 20: After refmac, R = 0.2055 (Rfree = 0.000) for 3076 atoms. Found 12 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3281 seeds are put forward Round 1: 204 peptides, 35 chains. Longest chain 16 peptides. Score 0.403 Round 2: 227 peptides, 36 chains. Longest chain 21 peptides. Score 0.462 Round 3: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.482 Round 4: 228 peptides, 36 chains. Longest chain 18 peptides. Score 0.465 Round 5: 241 peptides, 34 chains. Longest chain 24 peptides. Score 0.528 Taking the results from Round 5 Chains 34, Residues 207, Estimated correctness of the model 20.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 7002 restraints for refining 3095 atoms. 6208 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2285 (Rfree = 0.000) for 3095 atoms. Found 17 (27 requested) and removed 18 (13 requested) atoms. Cycle 22: After refmac, R = 0.2212 (Rfree = 0.000) for 3086 atoms. Found 7 (27 requested) and removed 17 (13 requested) atoms. Cycle 23: After refmac, R = 0.2153 (Rfree = 0.000) for 3072 atoms. Found 13 (27 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.2652 (Rfree = 0.000) for 3069 atoms. Found 27 (27 requested) and removed 17 (13 requested) atoms. Cycle 25: After refmac, R = 0.2422 (Rfree = 0.000) for 3068 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.11 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3299 seeds are put forward Round 1: 172 peptides, 33 chains. Longest chain 17 peptides. Score 0.322 Round 2: 209 peptides, 34 chains. Longest chain 19 peptides. Score 0.433 Round 3: 204 peptides, 34 chains. Longest chain 13 peptides. Score 0.417 Round 4: 217 peptides, 29 chains. Longest chain 23 peptides. Score 0.523 Round 5: 205 peptides, 31 chains. Longest chain 16 peptides. Score 0.461 Taking the results from Round 4 Chains 30, Residues 188, Estimated correctness of the model 18.7 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6791 restraints for refining 3096 atoms. 6022 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2243 (Rfree = 0.000) for 3096 atoms. Found 27 (27 requested) and removed 15 (13 requested) atoms. Cycle 27: After refmac, R = 0.2121 (Rfree = 0.000) for 3098 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 28: After refmac, R = 0.2085 (Rfree = 0.000) for 3084 atoms. Found 21 (27 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 3081 atoms. Found 13 (27 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1940 (Rfree = 0.000) for 3068 atoms. Found 11 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.05 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 3253 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 13 peptides. Score 0.321 Round 2: 217 peptides, 39 chains. Longest chain 12 peptides. Score 0.389 Round 3: 220 peptides, 38 chains. Longest chain 13 peptides. Score 0.412 Round 4: 221 peptides, 37 chains. Longest chain 13 peptides. Score 0.429 Round 5: 212 peptides, 36 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 4 Chains 37, Residues 184, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 7082 restraints for refining 3095 atoms. 6370 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2198 (Rfree = 0.000) for 3095 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. Cycle 32: After refmac, R = 0.2040 (Rfree = 0.000) for 3090 atoms. Found 11 (27 requested) and removed 17 (13 requested) atoms. Cycle 33: After refmac, R = 0.2005 (Rfree = 0.000) for 3081 atoms. Found 21 (27 requested) and removed 14 (13 requested) atoms. Cycle 34: After refmac, R = 0.2166 (Rfree = 0.000) for 3082 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 35: After refmac, R = 0.1855 (Rfree = 0.000) for 3079 atoms. Found 6 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.09 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3244 seeds are put forward Round 1: 176 peptides, 34 chains. Longest chain 12 peptides. Score 0.321 Round 2: 205 peptides, 34 chains. Longest chain 15 peptides. Score 0.420 Round 3: 200 peptides, 35 chains. Longest chain 15 peptides. Score 0.389 Round 4: 198 peptides, 33 chains. Longest chain 15 peptides. Score 0.411 Round 5: 200 peptides, 34 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 2 Chains 34, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6998 restraints for refining 3095 atoms. 6348 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2013 (Rfree = 0.000) for 3095 atoms. Found 22 (27 requested) and removed 20 (13 requested) atoms. Cycle 37: After refmac, R = 0.2266 (Rfree = 0.000) for 3095 atoms. Found 24 (27 requested) and removed 19 (13 requested) atoms. Cycle 38: After refmac, R = 0.1887 (Rfree = 0.000) for 3095 atoms. Found 10 (27 requested) and removed 17 (13 requested) atoms. Cycle 39: After refmac, R = 0.2297 (Rfree = 0.000) for 3080 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. Cycle 40: After refmac, R = 0.1812 (Rfree = 0.000) for 3084 atoms. Found 12 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.07 Search for helices and strands: 0 residues in 0 chains, 3221 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3238 seeds are put forward Round 1: 182 peptides, 37 chains. Longest chain 10 peptides. Score 0.297 Round 2: 182 peptides, 32 chains. Longest chain 13 peptides. Score 0.372 Round 3: 192 peptides, 32 chains. Longest chain 13 peptides. Score 0.406 Round 4: 206 peptides, 28 chains. Longest chain 22 peptides. Score 0.505 Round 5: 199 peptides, 32 chains. Longest chain 12 peptides. Score 0.429 Taking the results from Round 4 Chains 29, Residues 178, Estimated correctness of the model 12.9 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.85 % complete ) and 6714 restraints for refining 3096 atoms. 5964 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2206 (Rfree = 0.000) for 3096 atoms. Found 16 (27 requested) and removed 36 (13 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 3066 atoms. Found 22 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 3069 atoms. Found 17 (27 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.1798 (Rfree = 0.000) for 3065 atoms. Found 8 (27 requested) and removed 14 (13 requested) atoms. Cycle 45: After refmac, R = 0.1858 (Rfree = 0.000) for 3057 atoms. Found 15 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.10 Search for helices and strands: 0 residues in 0 chains, 3215 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3229 seeds are put forward Round 1: 167 peptides, 32 chains. Longest chain 11 peptides. Score 0.319 Round 2: 183 peptides, 30 chains. Longest chain 12 peptides. Score 0.405 Round 3: 193 peptides, 28 chains. Longest chain 19 peptides. Score 0.465 Round 4: 190 peptides, 27 chains. Longest chain 18 peptides. Score 0.470 Round 5: 176 peptides, 26 chains. Longest chain 17 peptides. Score 0.440 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 163, Estimated correctness of the model 1.4 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1zkg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.85 % complete ) and 6961 restraints for refining 3096 atoms. 6336 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1991 (Rfree = 0.000) for 3096 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1963 (Rfree = 0.000) for 3081 atoms. Found 0 (27 requested) and removed 9 (13 requested) atoms. Cycle 48: After refmac, R = 0.1911 (Rfree = 0.000) for 3068 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1853 (Rfree = 0.000) for 3053 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:02:32 GMT 2018 Job finished. TimeTaking 35.14 Used memory is bytes: 4001088