Mon 24 Dec 07:37:55 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zkg-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-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 07:37:59 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-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 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-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-3.4-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 3.400 Wilson plot Bfac: 76.69 6674 reflections ( 99.82 % complete ) and 0 restraints for refining 3766 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3339 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2924 (Rfree = 0.000) for 3766 atoms. Found 28 (28 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 3891 seeds are put forward NCS extension: 0 residues added, 3891 seeds are put forward Round 1: 171 peptides, 34 chains. Longest chain 10 peptides. Score 0.303 Round 2: 206 peptides, 34 chains. Longest chain 14 peptides. Score 0.423 Round 3: 222 peptides, 33 chains. Longest chain 16 peptides. Score 0.486 Round 4: 231 peptides, 30 chains. Longest chain 15 peptides. Score 0.550 Round 5: 237 peptides, 33 chains. Longest chain 19 peptides. Score 0.529 Taking the results from Round 4 Chains 30, Residues 201, Estimated correctness of the model 11.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7204 restraints for refining 3081 atoms. 6430 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2560 (Rfree = 0.000) for 3081 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 2: After refmac, R = 0.2389 (Rfree = 0.000) for 3044 atoms. Found 18 (23 requested) and removed 14 (11 requested) atoms. Cycle 3: After refmac, R = 0.2196 (Rfree = 0.000) for 3031 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2150 (Rfree = 0.000) for 3015 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. Cycle 5: After refmac, R = 0.2113 (Rfree = 0.000) for 3004 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 3163 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3179 seeds are put forward Round 1: 208 peptides, 37 chains. Longest chain 11 peptides. Score 0.387 Round 2: 234 peptides, 34 chains. Longest chain 17 peptides. Score 0.508 Round 3: 245 peptides, 37 chains. Longest chain 16 peptides. Score 0.502 Round 4: 239 peptides, 32 chains. Longest chain 19 peptides. Score 0.547 Round 5: 225 peptides, 38 chains. Longest chain 17 peptides. Score 0.428 Taking the results from Round 4 Chains 33, Residues 207, Estimated correctness of the model 10.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6692 restraints for refining 3040 atoms. 5821 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2382 (Rfree = 0.000) for 3040 atoms. Found 15 (22 requested) and removed 25 (11 requested) atoms. Cycle 7: After refmac, R = 0.2213 (Rfree = 0.000) for 3015 atoms. Found 11 (22 requested) and removed 14 (11 requested) atoms. Cycle 8: After refmac, R = 0.2132 (Rfree = 0.000) for 3006 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. Cycle 9: After refmac, R = 0.2132 (Rfree = 0.000) for 2990 atoms. Found 6 (22 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.2087 (Rfree = 0.000) for 2983 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3134 seeds are put forward Round 1: 195 peptides, 35 chains. Longest chain 12 peptides. Score 0.372 Round 2: 245 peptides, 38 chains. Longest chain 17 peptides. Score 0.489 Round 3: 228 peptides, 32 chains. Longest chain 14 peptides. Score 0.516 Round 4: 230 peptides, 29 chains. Longest chain 24 peptides. Score 0.559 Round 5: 223 peptides, 28 chains. Longest chain 25 peptides. Score 0.552 Taking the results from Round 4 Chains 29, Residues 201, Estimated correctness of the model 14.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6674 reflections ( 99.82 % complete ) and 7045 restraints for refining 3084 atoms. 6270 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2434 (Rfree = 0.000) for 3084 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 12: After refmac, R = 0.2134 (Rfree = 0.000) for 3077 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 13: After refmac, R = 0.2039 (Rfree = 0.000) for 3064 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.1996 (Rfree = 0.000) for 3049 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.1996 (Rfree = 0.000) for 3036 atoms. Found 3 (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, 3172 seeds are put forward NCS extension: 19 residues added (5 deleted due to clashes), 3191 seeds are put forward Round 1: 207 peptides, 35 chains. Longest chain 24 peptides. Score 0.412 Round 2: 208 peptides, 30 chains. Longest chain 22 peptides. Score 0.484 Round 3: 210 peptides, 27 chains. Longest chain 23 peptides. Score 0.529 Round 4: 218 peptides, 25 chains. Longest chain 27 peptides. Score 0.576 Round 5: 220 peptides, 28 chains. Longest chain 23 peptides. Score 0.544 Taking the results from Round 4 Chains 25, Residues 193, Estimated correctness of the model 20.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7146 restraints for refining 3084 atoms. 6399 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2332 (Rfree = 0.000) for 3084 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 17: After refmac, R = 0.2101 (Rfree = 0.000) for 3086 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. Cycle 18: After refmac, R = 0.2037 (Rfree = 0.000) for 3079 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2034 (Rfree = 0.000) for 3071 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2002 (Rfree = 0.000) for 3060 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 3205 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 3241 seeds are put forward Round 1: 207 peptides, 36 chains. Longest chain 12 peptides. Score 0.398 Round 2: 191 peptides, 29 chains. Longest chain 16 peptides. Score 0.445 Round 3: 190 peptides, 29 chains. Longest chain 13 peptides. Score 0.442 Round 4: 200 peptides, 28 chains. Longest chain 17 peptides. Score 0.487 Round 5: 197 peptides, 29 chains. Longest chain 20 peptides. Score 0.464 Taking the results from Round 4 Chains 29, Residues 172, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7166 restraints for refining 3084 atoms. 6476 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2302 (Rfree = 0.000) for 3084 atoms. Found 17 (23 requested) and removed 16 (11 requested) atoms. Cycle 22: After refmac, R = 0.2016 (Rfree = 0.000) for 3076 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1991 (Rfree = 0.000) for 3062 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 24: After refmac, R = 0.1969 (Rfree = 0.000) for 3049 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.1899 (Rfree = 0.000) for 3041 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 3196 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3220 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 10 peptides. Score 0.344 Round 2: 218 peptides, 35 chains. Longest chain 16 peptides. Score 0.447 Round 3: 218 peptides, 33 chains. Longest chain 18 peptides. Score 0.474 Round 4: 222 peptides, 36 chains. Longest chain 16 peptides. Score 0.446 Round 5: 218 peptides, 36 chains. Longest chain 13 peptides. Score 0.434 Taking the results from Round 3 Chains 33, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7064 restraints for refining 3082 atoms. 6357 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2327 (Rfree = 0.000) for 3082 atoms. Found 22 (23 requested) and removed 13 (11 requested) atoms. Cycle 27: After refmac, R = 0.2097 (Rfree = 0.000) for 3078 atoms. Found 16 (23 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.2039 (Rfree = 0.000) for 3077 atoms. Found 10 (23 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1993 (Rfree = 0.000) for 3065 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1959 (Rfree = 0.000) for 3058 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 3215 seeds are put forward Round 1: 174 peptides, 35 chains. Longest chain 10 peptides. Score 0.299 Round 2: 214 peptides, 37 chains. Longest chain 13 peptides. Score 0.407 Round 3: 212 peptides, 34 chains. Longest chain 20 peptides. Score 0.442 Round 4: 215 peptides, 37 chains. Longest chain 15 peptides. Score 0.410 Round 5: 206 peptides, 33 chains. Longest chain 21 peptides. Score 0.437 Taking the results from Round 3 Chains 34, Residues 178, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7016 restraints for refining 3083 atoms. 6318 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2329 (Rfree = 0.000) for 3083 atoms. Found 17 (23 requested) and removed 12 (11 requested) atoms. Cycle 32: After refmac, R = 0.2149 (Rfree = 0.000) for 3083 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2048 (Rfree = 0.000) for 3073 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2002 (Rfree = 0.000) for 3064 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1956 (Rfree = 0.000) for 3049 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 3.33 Search for helices and strands: 0 residues in 0 chains, 3191 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3213 seeds are put forward Round 1: 170 peptides, 34 chains. Longest chain 8 peptides. Score 0.299 Round 2: 176 peptides, 28 chains. Longest chain 12 peptides. Score 0.411 Round 3: 181 peptides, 27 chains. Longest chain 17 peptides. Score 0.442 Round 4: 198 peptides, 31 chains. Longest chain 11 peptides. Score 0.439 Round 5: 189 peptides, 29 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 3 Chains 29, Residues 154, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7086 restraints for refining 3084 atoms. 6447 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2297 (Rfree = 0.000) for 3084 atoms. Found 21 (23 requested) and removed 12 (11 requested) atoms. Cycle 37: After refmac, R = 0.2074 (Rfree = 0.000) for 3083 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. Cycle 38: After refmac, R = 0.2041 (Rfree = 0.000) for 3076 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.2008 (Rfree = 0.000) for 3068 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1968 (Rfree = 0.000) for 3060 atoms. Found 7 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 0 residues added, 3220 seeds are put forward Round 1: 162 peptides, 33 chains. Longest chain 15 peptides. Score 0.285 Round 2: 193 peptides, 31 chains. Longest chain 16 peptides. Score 0.423 Round 3: 194 peptides, 32 chains. Longest chain 16 peptides. Score 0.412 Round 4: 194 peptides, 34 chains. Longest chain 11 peptides. Score 0.384 Round 5: 189 peptides, 32 chains. Longest chain 11 peptides. Score 0.396 Taking the results from Round 2 Chains 31, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7113 restraints for refining 3083 atoms. 6496 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2217 (Rfree = 0.000) for 3083 atoms. Found 18 (23 requested) and removed 12 (11 requested) atoms. Cycle 42: After refmac, R = 0.2070 (Rfree = 0.000) for 3086 atoms. Found 11 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1955 (Rfree = 0.000) for 3083 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1949 (Rfree = 0.000) for 3071 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1815 (Rfree = 0.000) for 3066 atoms. Found 2 (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, 3205 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3231 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 10 peptides. Score 0.292 Round 2: 192 peptides, 32 chains. Longest chain 16 peptides. Score 0.406 Round 3: 190 peptides, 31 chains. Longest chain 12 peptides. Score 0.413 Round 4: 180 peptides, 26 chains. Longest chain 13 peptides. Score 0.453 Round 5: 163 peptides, 27 chains. Longest chain 11 peptides. Score 0.382 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 154, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence Sequence coverage is 5 % 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 7111 restraints for refining 3084 atoms. 6486 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2243 (Rfree = 0.000) for 3084 atoms. Found 0 (23 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.2112 (Rfree = 0.000) for 3069 atoms. Found 0 (23 requested) and removed 1 (11 requested) atoms. Cycle 48: After refmac, R = 0.2062 (Rfree = 0.000) for 3064 atoms. Found 0 (23 requested) and removed 1 (11 requested) atoms. Cycle 49: After refmac, R = 0.2011 (Rfree = 0.000) for 3063 atoms. TimeTaking 35.02