Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zkg-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zkg-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:07 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/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zkg-3.4-parrot-hancs/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-hancs.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-hancs.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 3781 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3343 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2819 (Rfree = 0.000) for 3781 atoms. Found 28 (28 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 3915 seeds are put forward NCS extension: 0 residues added, 3915 seeds are put forward Round 1: 206 peptides, 40 chains. Longest chain 14 peptides. Score 0.337 Round 2: 246 peptides, 38 chains. Longest chain 14 peptides. Score 0.492 Round 3: 241 peptides, 39 chains. Longest chain 14 peptides. Score 0.464 Round 4: 242 peptides, 33 chains. Longest chain 13 peptides. Score 0.543 Round 5: 241 peptides, 32 chains. Longest chain 14 peptides. Score 0.552 Taking the results from Round 5 Chains 34, Residues 209, Estimated correctness of the model 12.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6924 restraints for refining 3082 atoms. 6087 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 3082 atoms. Found 16 (23 requested) and removed 22 (11 requested) atoms. Cycle 2: After refmac, R = 0.2328 (Rfree = 0.000) for 3025 atoms. Found 10 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2269 (Rfree = 0.000) for 3001 atoms. Found 9 (22 requested) and removed 12 (11 requested) atoms. Cycle 4: After refmac, R = 0.2195 (Rfree = 0.000) for 2993 atoms. Found 4 (22 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2157 (Rfree = 0.000) for 2977 atoms. Found 3 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3125 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3140 seeds are put forward Round 1: 213 peptides, 36 chains. Longest chain 14 peptides. Score 0.418 Round 2: 246 peptides, 39 chains. Longest chain 17 peptides. Score 0.479 Round 3: 259 peptides, 36 chains. Longest chain 15 peptides. Score 0.553 Round 4: 256 peptides, 35 chains. Longest chain 21 peptides. Score 0.557 Round 5: 253 peptides, 32 chains. Longest chain 19 peptides. Score 0.584 Taking the results from Round 5 Chains 34, Residues 221, Estimated correctness of the model 23.4 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6696 restraints for refining 3076 atoms. 5776 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2558 (Rfree = 0.000) for 3076 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. Cycle 7: After refmac, R = 0.2314 (Rfree = 0.000) for 3058 atoms. Found 11 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2248 (Rfree = 0.000) for 3048 atoms. Found 8 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2185 (Rfree = 0.000) for 3038 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 3030 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 3181 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3198 seeds are put forward Round 1: 211 peptides, 34 chains. Longest chain 12 peptides. Score 0.439 Round 2: 248 peptides, 39 chains. Longest chain 13 peptides. Score 0.485 Round 3: 238 peptides, 32 chains. Longest chain 15 peptides. Score 0.544 Round 4: 244 peptides, 36 chains. Longest chain 12 peptides. Score 0.512 Round 5: 258 peptides, 33 chains. Longest chain 19 peptides. Score 0.585 Taking the results from Round 5 Chains 33, Residues 225, Estimated correctness of the model 23.7 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6674 reflections ( 99.82 % complete ) and 6966 restraints for refining 3083 atoms. 6059 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2454 (Rfree = 0.000) for 3083 atoms. Found 19 (23 requested) and removed 21 (11 requested) atoms. Cycle 12: After refmac, R = 0.2261 (Rfree = 0.000) for 3062 atoms. Found 12 (23 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.2224 (Rfree = 0.000) for 3054 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2194 (Rfree = 0.000) for 3043 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.2151 (Rfree = 0.000) for 3029 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.27 Search for helices and strands: 0 residues in 0 chains, 3170 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3186 seeds are put forward Round 1: 233 peptides, 42 chains. Longest chain 11 peptides. Score 0.399 Round 2: 244 peptides, 37 chains. Longest chain 14 peptides. Score 0.499 Round 3: 243 peptides, 33 chains. Longest chain 16 peptides. Score 0.546 Round 4: 244 peptides, 34 chains. Longest chain 16 peptides. Score 0.536 Round 5: 244 peptides, 34 chains. Longest chain 15 peptides. Score 0.536 Taking the results from Round 3 Chains 34, Residues 210, Estimated correctness of the model 10.1 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 6845 restraints for refining 3084 atoms. 5971 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2601 (Rfree = 0.000) for 3084 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2363 (Rfree = 0.000) for 3078 atoms. Found 20 (23 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2250 (Rfree = 0.000) for 3074 atoms. Found 7 (23 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2207 (Rfree = 0.000) for 3068 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2187 (Rfree = 0.000) for 3058 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3210 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 3214 seeds are put forward Round 1: 238 peptides, 40 chains. Longest chain 15 peptides. Score 0.442 Round 2: 255 peptides, 37 chains. Longest chain 12 peptides. Score 0.530 Round 3: 232 peptides, 34 chains. Longest chain 13 peptides. Score 0.502 Round 4: 243 peptides, 34 chains. Longest chain 14 peptides. Score 0.533 Round 5: 241 peptides, 35 chains. Longest chain 15 peptides. Score 0.515 Taking the results from Round 4 Chains 34, Residues 209, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6674 reflections ( 99.82 % complete ) and 7038 restraints for refining 3083 atoms. 6236 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2447 (Rfree = 0.000) for 3083 atoms. Found 21 (23 requested) and removed 18 (11 requested) atoms. Cycle 22: After refmac, R = 0.2232 (Rfree = 0.000) for 3081 atoms. Found 9 (23 requested) and removed 15 (11 requested) atoms. Cycle 23: After refmac, R = 0.2202 (Rfree = 0.000) for 3074 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 24: After refmac, R = 0.2145 (Rfree = 0.000) for 3063 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2106 (Rfree = 0.000) for 3051 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3216 seeds are put forward Round 1: 201 peptides, 37 chains. Longest chain 13 peptides. Score 0.364 Round 2: 227 peptides, 35 chains. Longest chain 14 peptides. Score 0.475 Round 3: 235 peptides, 35 chains. Longest chain 23 peptides. Score 0.498 Round 4: 232 peptides, 34 chains. Longest chain 14 peptides. Score 0.502 Round 5: 231 peptides, 33 chains. Longest chain 25 peptides. Score 0.512 Taking the results from Round 5 Chains 33, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7090 restraints for refining 3084 atoms. 6331 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2497 (Rfree = 0.000) for 3084 atoms. Found 20 (23 requested) and removed 12 (11 requested) atoms. Cycle 27: After refmac, R = 0.2229 (Rfree = 0.000) for 3083 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2151 (Rfree = 0.000) for 3071 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2165 (Rfree = 0.000) for 3064 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2125 (Rfree = 0.000) for 3051 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 3190 seeds are put forward NCS extension: 55 residues added (5 deleted due to clashes), 3245 seeds are put forward Round 1: 171 peptides, 34 chains. Longest chain 10 peptides. Score 0.303 Round 2: 196 peptides, 35 chains. Longest chain 16 peptides. Score 0.376 Round 3: 214 peptides, 34 chains. Longest chain 15 peptides. Score 0.448 Round 4: 218 peptides, 33 chains. Longest chain 15 peptides. Score 0.474 Round 5: 201 peptides, 31 chains. Longest chain 11 peptides. Score 0.449 Taking the results from Round 4 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 7189 restraints for refining 3084 atoms. 6482 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2422 (Rfree = 0.000) for 3084 atoms. Found 18 (23 requested) and removed 11 (11 requested) atoms. Cycle 32: After refmac, R = 0.2225 (Rfree = 0.000) for 3086 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.2136 (Rfree = 0.000) for 3076 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.2101 (Rfree = 0.000) for 3066 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2080 (Rfree = 0.000) for 3055 atoms. Found 3 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3221 seeds are put forward Round 1: 159 peptides, 31 chains. Longest chain 15 peptides. Score 0.306 Round 2: 198 peptides, 36 chains. Longest chain 16 peptides. Score 0.368 Round 3: 191 peptides, 34 chains. Longest chain 16 peptides. Score 0.373 Round 4: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.369 Round 5: 185 peptides, 32 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 5 Chains 32, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7316 restraints for refining 3084 atoms. 6736 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2292 (Rfree = 0.000) for 3084 atoms. Found 19 (23 requested) and removed 11 (11 requested) atoms. Cycle 37: After refmac, R = 0.2154 (Rfree = 0.000) for 3087 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2148 (Rfree = 0.000) for 3074 atoms. Found 10 (23 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.2101 (Rfree = 0.000) for 3070 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2048 (Rfree = 0.000) for 3060 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 3207 seeds are put forward NCS extension: 5 residues added (1 deleted due to clashes), 3212 seeds are put forward Round 1: 150 peptides, 27 chains. Longest chain 12 peptides. Score 0.336 Round 2: 163 peptides, 30 chains. Longest chain 13 peptides. Score 0.336 Round 3: 174 peptides, 29 chains. Longest chain 12 peptides. Score 0.389 Round 4: 181 peptides, 30 chains. Longest chain 12 peptides. Score 0.398 Round 5: 194 peptides, 30 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 5 Chains 30, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6674 reflections ( 99.82 % complete ) and 7161 restraints for refining 3082 atoms. 6535 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2311 (Rfree = 0.000) for 3082 atoms. Found 13 (23 requested) and removed 14 (11 requested) atoms. Cycle 42: After refmac, R = 0.2144 (Rfree = 0.000) for 3074 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2107 (Rfree = 0.000) for 3069 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. Cycle 44: After refmac, R = 0.2082 (Rfree = 0.000) for 3058 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 3053 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 3220 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3236 seeds are put forward Round 1: 165 peptides, 31 chains. Longest chain 10 peptides. Score 0.327 Round 2: 163 peptides, 30 chains. Longest chain 11 peptides. Score 0.336 Round 3: 169 peptides, 31 chains. Longest chain 10 peptides. Score 0.342 Round 4: 169 peptides, 30 chains. Longest chain 15 peptides. Score 0.357 Round 5: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.383 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 133, 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 7333 restraints for refining 3084 atoms. 6827 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2372 (Rfree = 0.000) for 3084 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2207 (Rfree = 0.000) for 3065 atoms. Found 0 (23 requested) and removed 8 (11 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2134 (Rfree = 0.000) for 3054 atoms. Found 0 (23 requested) and removed 7 (11 requested) atoms. Cycle 49: After refmac, R = 0.2082 (Rfree = 0.000) for 3042 atoms. Found 0 (23 requested) and removed 4 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:22:04 GMT 2018 Job finished. TimeTaking 54.12