null Mon 24 Dec 07:32:04 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 1vmf-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-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/1vmf-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-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 07:32:09 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/1vmf-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-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 326 and 0 Target number of residues in the AU: 326 Target solvent content: 0.6119 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-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: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.65 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: 67.531 3.400 Wilson plot Bfac: 57.67 6666 reflections ( 99.72 % complete ) and 0 restraints for refining 3865 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2998 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2950 (Rfree = 0.000) for 3865 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 0 residues added, 3946 seeds are put forward Round 1: 209 peptides, 38 chains. Longest chain 12 peptides. Score 0.388 Round 2: 261 peptides, 39 chains. Longest chain 16 peptides. Score 0.540 Round 3: 276 peptides, 38 chains. Longest chain 15 peptides. Score 0.593 Round 4: 286 peptides, 36 chains. Longest chain 20 peptides. Score 0.640 Round 5: 276 peptides, 30 chains. Longest chain 38 peptides. Score 0.679 Taking the results from Round 5 Chains 30, Residues 246, Estimated correctness of the model 52.3 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6777 restraints for refining 3161 atoms. 5764 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 3161 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. Cycle 2: After refmac, R = 0.2703 (Rfree = 0.000) for 3142 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 3: After refmac, R = 0.2604 (Rfree = 0.000) for 3126 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 4: After refmac, R = 0.2514 (Rfree = 0.000) for 3126 atoms. Found 11 (23 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2260 (Rfree = 0.000) for 3113 atoms. Found 8 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 65 residues added (1 deleted due to clashes), 3277 seeds are put forward Round 1: 247 peptides, 35 chains. Longest chain 15 peptides. Score 0.550 Round 2: 272 peptides, 33 chains. Longest chain 19 peptides. Score 0.639 Round 3: 278 peptides, 29 chains. Longest chain 24 peptides. Score 0.694 Round 4: 273 peptides, 31 chains. Longest chain 21 peptides. Score 0.662 Round 5: 267 peptides, 29 chains. Longest chain 19 peptides. Score 0.670 Taking the results from Round 3 Chains 29, Residues 249, Estimated correctness of the model 56.3 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6905 restraints for refining 3163 atoms. 5886 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2391 (Rfree = 0.000) for 3163 atoms. Found 16 (23 requested) and removed 16 (11 requested) atoms. Cycle 7: After refmac, R = 0.2365 (Rfree = 0.000) for 3147 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2042 (Rfree = 0.000) for 3143 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 9: After refmac, R = 0.2247 (Rfree = 0.000) for 3131 atoms. Found 12 (23 requested) and removed 17 (11 requested) atoms. Cycle 10: After refmac, R = 0.2158 (Rfree = 0.000) for 3121 atoms. Found 12 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3234 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3254 seeds are put forward Round 1: 246 peptides, 38 chains. Longest chain 13 peptides. Score 0.509 Round 2: 263 peptides, 31 chains. Longest chain 20 peptides. Score 0.639 Round 3: 288 peptides, 31 chains. Longest chain 21 peptides. Score 0.695 Round 4: 277 peptides, 29 chains. Longest chain 28 peptides. Score 0.691 Round 5: 290 peptides, 32 chains. Longest chain 30 peptides. Score 0.689 Taking the results from Round 3 Chains 31, Residues 257, Estimated correctness of the model 56.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6949 restraints for refining 3164 atoms. 5952 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2206 (Rfree = 0.000) for 3164 atoms. Found 14 (23 requested) and removed 11 (11 requested) atoms. Cycle 12: After refmac, R = 0.2110 (Rfree = 0.000) for 3158 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2140 (Rfree = 0.000) for 3151 atoms. Found 15 (23 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.2178 (Rfree = 0.000) for 3150 atoms. Found 18 (23 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.1931 (Rfree = 0.000) for 3149 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3242 seeds are put forward Round 1: 253 peptides, 31 chains. Longest chain 14 peptides. Score 0.614 Round 2: 267 peptides, 29 chains. Longest chain 27 peptides. Score 0.670 Round 3: 281 peptides, 30 chains. Longest chain 23 peptides. Score 0.690 Round 4: 276 peptides, 30 chains. Longest chain 27 peptides. Score 0.679 Round 5: 274 peptides, 31 chains. Longest chain 23 peptides. Score 0.665 Taking the results from Round 3 Chains 30, Residues 251, Estimated correctness of the model 55.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6956 restraints for refining 3161 atoms. 5982 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2174 (Rfree = 0.000) for 3161 atoms. Found 18 (23 requested) and removed 17 (11 requested) atoms. Cycle 17: After refmac, R = 0.1997 (Rfree = 0.000) for 3157 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2468 (Rfree = 0.000) for 3144 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. Cycle 19: After refmac, R = 0.2024 (Rfree = 0.000) for 3151 atoms. Found 7 (23 requested) and removed 18 (11 requested) atoms. Cycle 20: After refmac, R = 0.2031 (Rfree = 0.000) for 3139 atoms. Found 10 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3235 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3258 seeds are put forward Round 1: 235 peptides, 29 chains. Longest chain 21 peptides. Score 0.591 Round 2: 259 peptides, 29 chains. Longest chain 24 peptides. Score 0.651 Round 3: 277 peptides, 31 chains. Longest chain 26 peptides. Score 0.671 Round 4: 271 peptides, 28 chains. Longest chain 23 peptides. Score 0.689 Round 5: 270 peptides, 29 chains. Longest chain 25 peptides. Score 0.676 Taking the results from Round 4 Chains 28, Residues 243, Estimated correctness of the model 55.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 6943 restraints for refining 3164 atoms. 5999 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2168 (Rfree = 0.000) for 3164 atoms. Found 12 (23 requested) and removed 11 (11 requested) atoms. Cycle 22: After refmac, R = 0.2040 (Rfree = 0.000) for 3160 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 23: After refmac, R = 0.2034 (Rfree = 0.000) for 3150 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1925 (Rfree = 0.000) for 3143 atoms. Found 5 (23 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.1817 (Rfree = 0.000) for 3131 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 3.27 Search for helices and strands: 0 residues in 0 chains, 3211 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 3231 seeds are put forward Round 1: 216 peptides, 31 chains. Longest chain 15 peptides. Score 0.511 Round 2: 248 peptides, 25 chains. Longest chain 27 peptides. Score 0.669 Round 3: 244 peptides, 25 chains. Longest chain 23 peptides. Score 0.660 Round 4: 263 peptides, 30 chains. Longest chain 24 peptides. Score 0.650 Round 5: 245 peptides, 26 chains. Longest chain 19 peptides. Score 0.651 Taking the results from Round 2 Chains 27, Residues 223, Estimated correctness of the model 49.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7033 restraints for refining 3164 atoms. 6111 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2082 (Rfree = 0.000) for 3164 atoms. Found 13 (23 requested) and removed 13 (11 requested) atoms. Cycle 27: After refmac, R = 0.1985 (Rfree = 0.000) for 3162 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.1914 (Rfree = 0.000) for 3153 atoms. Found 1 (23 requested) and removed 12 (11 requested) atoms. Cycle 29: After refmac, R = 0.1898 (Rfree = 0.000) for 3142 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 3134 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 3233 seeds are put forward Round 1: 199 peptides, 26 chains. Longest chain 16 peptides. Score 0.527 Round 2: 239 peptides, 30 chains. Longest chain 23 peptides. Score 0.590 Round 3: 248 peptides, 28 chains. Longest chain 19 peptides. Score 0.636 Round 4: 250 peptides, 33 chains. Longest chain 13 peptides. Score 0.583 Round 5: 239 peptides, 27 chains. Longest chain 18 peptides. Score 0.625 Taking the results from Round 3 Chains 28, Residues 220, Estimated correctness of the model 40.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7143 restraints for refining 3164 atoms. 6291 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2057 (Rfree = 0.000) for 3164 atoms. Found 13 (23 requested) and removed 12 (11 requested) atoms. Cycle 32: After refmac, R = 0.1970 (Rfree = 0.000) for 3163 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1935 (Rfree = 0.000) for 3153 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1934 (Rfree = 0.000) for 3142 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.1915 (Rfree = 0.000) for 3136 atoms. Found 1 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.25 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3223 seeds are put forward Round 1: 208 peptides, 31 chains. Longest chain 14 peptides. Score 0.486 Round 2: 238 peptides, 31 chains. Longest chain 15 peptides. Score 0.575 Round 3: 259 peptides, 32 chains. Longest chain 19 peptides. Score 0.618 Round 4: 245 peptides, 30 chains. Longest chain 18 peptides. Score 0.605 Round 5: 264 peptides, 33 chains. Longest chain 18 peptides. Score 0.619 Taking the results from Round 5 Chains 33, Residues 231, Estimated correctness of the model 34.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7116 restraints for refining 3164 atoms. 6225 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2083 (Rfree = 0.000) for 3164 atoms. Found 6 (23 requested) and removed 12 (11 requested) atoms. Cycle 37: After refmac, R = 0.1909 (Rfree = 0.000) for 3149 atoms. Found 8 (23 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.1815 (Rfree = 0.000) for 3143 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1797 (Rfree = 0.000) for 3133 atoms. Found 5 (23 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1784 (Rfree = 0.000) for 3126 atoms. Found 9 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 3.26 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3230 seeds are put forward Round 1: 217 peptides, 32 chains. Longest chain 16 peptides. Score 0.500 Round 2: 232 peptides, 32 chains. Longest chain 14 peptides. Score 0.545 Round 3: 232 peptides, 34 chains. Longest chain 18 peptides. Score 0.519 Round 4: 233 peptides, 30 chains. Longest chain 20 peptides. Score 0.573 Round 5: 219 peptides, 24 chains. Longest chain 16 peptides. Score 0.609 Taking the results from Round 5 Chains 24, Residues 195, Estimated correctness of the model 31.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6666 reflections ( 99.72 % complete ) and 7237 restraints for refining 3164 atoms. 6481 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2278 (Rfree = 0.000) for 3164 atoms. Found 12 (23 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.2156 (Rfree = 0.000) for 3159 atoms. Found 12 (23 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2042 (Rfree = 0.000) for 3155 atoms. Found 6 (23 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1942 (Rfree = 0.000) for 3147 atoms. Found 4 (23 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.2144 (Rfree = 0.000) for 3136 atoms. Found 19 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.29 Search for helices and strands: 0 residues in 0 chains, 3218 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3241 seeds are put forward Round 1: 199 peptides, 33 chains. Longest chain 14 peptides. Score 0.427 Round 2: 232 peptides, 29 chains. Longest chain 17 peptides. Score 0.583 Round 3: 230 peptides, 27 chains. Longest chain 17 peptides. Score 0.602 Round 4: 241 peptides, 27 chains. Longest chain 19 peptides. Score 0.630 Round 5: 222 peptides, 27 chains. Longest chain 22 peptides. Score 0.580 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 214, Estimated correctness of the model 38.2 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vmf-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6666 reflections ( 99.72 % complete ) and 6908 restraints for refining 3164 atoms. 6015 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2158 (Rfree = 0.000) for 3164 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2100 (Rfree = 0.000) for 3146 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2014 (Rfree = 0.000) for 3132 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2002 (Rfree = 0.000) for 3118 atoms. Found 0 (23 requested) and removed 6 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:08:40 GMT 2018 Job finished. TimeTaking 36.59 Used memory is bytes: 10745608