null Mon 24 Dec 00:35:35 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 1zkg-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zkg-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-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/1zkg-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-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 00:35:39 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/1zkg-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zkg-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 317 and 0 Target number of residues in the AU: 317 Target solvent content: 0.6478 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-3.4-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: 50.537 87.114 59.148 90.000 110.732 90.000 Input sequence file: 1zkg-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 76.69 6674 reflections ( 99.82 % complete ) and 0 restraints for refining 3734 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3367 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2921 (Rfree = 0.000) for 3734 atoms. Found 28 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 3862 seeds are put forward NCS extension: 0 residues added, 3862 seeds are put forward Round 1: 184 peptides, 36 chains. Longest chain 11 peptides. Score 0.319 Round 2: 228 peptides, 37 chains. Longest chain 13 peptides. Score 0.451 Round 3: 236 peptides, 34 chains. Longest chain 20 peptides. Score 0.514 Round 4: 246 peptides, 35 chains. Longest chain 21 peptides. Score 0.530 Round 5: 246 peptides, 29 chains. Longest chain 28 peptides. Score 0.600 Taking the results from Round 5 Chains 29, Residues 217, Estimated correctness of the model 28.7 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6891 restraints for refining 3082 atoms. 6011 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2481 (Rfree = 0.000) for 3082 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 2: After refmac, R = 0.2284 (Rfree = 0.000) for 3022 atoms. Found 13 (23 requested) and removed 15 (11 requested) atoms. Cycle 3: After refmac, R = 0.2204 (Rfree = 0.000) for 3007 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 2987 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. Cycle 5: After refmac, R = 0.2127 (Rfree = 0.000) for 2977 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3135 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 3150 seeds are put forward Round 1: 220 peptides, 33 chains. Longest chain 18 peptides. Score 0.480 Round 2: 251 peptides, 32 chains. Longest chain 21 peptides. Score 0.579 Round 3: 260 peptides, 29 chains. Longest chain 23 peptides. Score 0.634 Round 4: 249 peptides, 31 chains. Longest chain 21 peptides. Score 0.585 Round 5: 257 peptides, 27 chains. Longest chain 24 peptides. Score 0.648 Taking the results from Round 5 Chains 27, Residues 230, Estimated correctness of the model 43.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6732 restraints for refining 3025 atoms. 5839 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2357 (Rfree = 0.000) for 3025 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 7: After refmac, R = 0.2176 (Rfree = 0.000) for 3014 atoms. Found 10 (22 requested) and removed 12 (11 requested) atoms. Cycle 8: After refmac, R = 0.2127 (Rfree = 0.000) for 3007 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 9: After refmac, R = 0.2102 (Rfree = 0.000) for 3000 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.2092 (Rfree = 0.000) for 2989 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3157 seeds are put forward NCS extension: 34 residues added (5 deleted due to clashes), 3191 seeds are put forward Round 1: 216 peptides, 41 chains. Longest chain 11 peptides. Score 0.357 Round 2: 236 peptides, 33 chains. Longest chain 13 peptides. Score 0.526 Round 3: 227 peptides, 33 chains. Longest chain 14 peptides. Score 0.501 Round 4: 240 peptides, 35 chains. Longest chain 14 peptides. Score 0.513 Round 5: 219 peptides, 33 chains. Longest chain 22 peptides. Score 0.477 Taking the results from Round 2 Chains 33, Residues 203, Estimated correctness of the model 2.7 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7057 restraints for refining 3078 atoms. 6257 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2422 (Rfree = 0.000) for 3078 atoms. Found 18 (23 requested) and removed 21 (11 requested) atoms. Cycle 12: After refmac, R = 0.2224 (Rfree = 0.000) for 3065 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 3050 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2122 (Rfree = 0.000) for 3044 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2060 (Rfree = 0.000) for 3036 atoms. Found 2 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3202 seeds are put forward Round 1: 196 peptides, 39 chains. Longest chain 9 peptides. Score 0.317 Round 2: 239 peptides, 34 chains. Longest chain 15 peptides. Score 0.522 Round 3: 248 peptides, 34 chains. Longest chain 21 peptides. Score 0.547 Round 4: 231 peptides, 33 chains. Longest chain 19 peptides. Score 0.512 Round 5: 239 peptides, 30 chains. Longest chain 21 peptides. Score 0.571 Taking the results from Round 5 Chains 31, Residues 209, Estimated correctness of the model 18.9 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6948 restraints for refining 3084 atoms. 6118 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2479 (Rfree = 0.000) for 3084 atoms. Found 22 (23 requested) and removed 19 (11 requested) atoms. Cycle 17: After refmac, R = 0.2238 (Rfree = 0.000) for 3077 atoms. Found 12 (23 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.2138 (Rfree = 0.000) for 3070 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2103 (Rfree = 0.000) for 3058 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2074 (Rfree = 0.000) for 3048 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3192 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3220 seeds are put forward Round 1: 200 peptides, 33 chains. Longest chain 11 peptides. Score 0.418 Round 2: 229 peptides, 36 chains. Longest chain 15 peptides. Score 0.468 Round 3: 237 peptides, 37 chains. Longest chain 12 peptides. Score 0.479 Round 4: 231 peptides, 32 chains. Longest chain 21 peptides. Score 0.525 Round 5: 229 peptides, 35 chains. Longest chain 12 peptides. Score 0.481 Taking the results from Round 4 Chains 32, Residues 199, Estimated correctness of the model 2.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7222 restraints for refining 3084 atoms. 6458 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2405 (Rfree = 0.000) for 3084 atoms. Found 20 (23 requested) and removed 15 (11 requested) atoms. Cycle 22: After refmac, R = 0.2185 (Rfree = 0.000) for 3079 atoms. Found 7 (23 requested) and removed 13 (11 requested) atoms. Cycle 23: After refmac, R = 0.2164 (Rfree = 0.000) for 3066 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2088 (Rfree = 0.000) for 3054 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2076 (Rfree = 0.000) for 3046 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 3186 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3202 seeds are put forward Round 1: 210 peptides, 41 chains. Longest chain 12 peptides. Score 0.337 Round 2: 249 peptides, 42 chains. Longest chain 11 peptides. Score 0.450 Round 3: 232 peptides, 38 chains. Longest chain 15 peptides. Score 0.450 Round 4: 239 peptides, 37 chains. Longest chain 19 peptides. Score 0.484 Round 5: 221 peptides, 33 chains. Longest chain 19 peptides. Score 0.483 Taking the results from Round 4 Chains 38, Residues 202, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6914 restraints for refining 3083 atoms. 6112 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2384 (Rfree = 0.000) for 3083 atoms. Found 17 (23 requested) and removed 18 (11 requested) atoms. Cycle 27: After refmac, R = 0.2136 (Rfree = 0.000) for 3075 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2055 (Rfree = 0.000) for 3067 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.2030 (Rfree = 0.000) for 3057 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2001 (Rfree = 0.000) for 3045 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3215 seeds are put forward Round 1: 175 peptides, 36 chains. Longest chain 10 peptides. Score 0.287 Round 2: 204 peptides, 35 chains. Longest chain 17 peptides. Score 0.403 Round 3: 212 peptides, 36 chains. Longest chain 11 peptides. Score 0.414 Round 4: 203 peptides, 31 chains. Longest chain 19 peptides. Score 0.455 Round 5: 201 peptides, 30 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 5 Chains 32, Residues 171, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7205 restraints for refining 3084 atoms. 6493 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2468 (Rfree = 0.000) for 3084 atoms. Found 20 (23 requested) and removed 21 (11 requested) atoms. Cycle 32: After refmac, R = 0.2260 (Rfree = 0.000) for 3078 atoms. Found 11 (23 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2186 (Rfree = 0.000) for 3072 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2136 (Rfree = 0.000) for 3065 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.2058 (Rfree = 0.000) for 3055 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.35 Search for helices and strands: 0 residues in 0 chains, 3204 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3216 seeds are put forward Round 1: 162 peptides, 33 chains. Longest chain 13 peptides. Score 0.285 Round 2: 175 peptides, 33 chains. Longest chain 9 peptides. Score 0.333 Round 3: 195 peptides, 34 chains. Longest chain 14 peptides. Score 0.387 Round 4: 195 peptides, 35 chains. Longest chain 10 peptides. Score 0.372 Round 5: 203 peptides, 34 chains. Longest chain 15 peptides. Score 0.413 Taking the results from Round 5 Chains 34, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7372 restraints for refining 3084 atoms. 6730 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2338 (Rfree = 0.000) for 3084 atoms. Found 20 (23 requested) and removed 15 (11 requested) atoms. Cycle 37: After refmac, R = 0.2173 (Rfree = 0.000) for 3087 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2109 (Rfree = 0.000) for 3071 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2058 (Rfree = 0.000) for 3063 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.2041 (Rfree = 0.000) for 3051 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3230 seeds are put forward Round 1: 162 peptides, 33 chains. Longest chain 10 peptides. Score 0.285 Round 2: 181 peptides, 36 chains. Longest chain 9 peptides. Score 0.309 Round 3: 186 peptides, 34 chains. Longest chain 13 peptides. Score 0.356 Round 4: 180 peptides, 32 chains. Longest chain 10 peptides. Score 0.365 Round 5: 179 peptides, 30 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 5 Chains 30, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7397 restraints for refining 3084 atoms. 6831 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2393 (Rfree = 0.000) for 3084 atoms. Found 19 (23 requested) and removed 16 (11 requested) atoms. Cycle 42: After refmac, R = 0.2246 (Rfree = 0.000) for 3082 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 3070 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2119 (Rfree = 0.000) for 3064 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2101 (Rfree = 0.000) for 3050 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3207 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 14 peptides. Score 0.282 Round 2: 162 peptides, 29 chains. Longest chain 12 peptides. Score 0.348 Round 3: 173 peptides, 31 chains. Longest chain 12 peptides. Score 0.356 Round 4: 169 peptides, 29 chains. Longest chain 10 peptides. Score 0.372 Round 5: 167 peptides, 27 chains. Longest chain 12 peptides. Score 0.395 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 140, 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 1zkg-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6674 reflections ( 99.82 % complete ) and 7336 restraints for refining 3068 atoms. 6803 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2297 (Rfree = 0.000) for 3068 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2242 (Rfree = 0.000) for 3054 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 48: After refmac, R = 0.2168 (Rfree = 0.000) for 3042 atoms. Found 0 (22 requested) and removed 5 (11 requested) atoms. Cycle 49: After refmac, R = 0.2151 (Rfree = 0.000) for 3033 atoms. Found 0 (22 requested) and removed 1 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:09:45 GMT 2018 Job finished. TimeTaking 34.17 Used memory is bytes: 2044400