null Sun 23 Dec 22:23:02 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 1vpy-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.6-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/1vpy-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.6-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 ============================================================ Sun 23 Dec 22:23:11 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/1vpy-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.6-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 263 and 0 Target number of residues in the AU: 263 Target solvent content: 0.6384 Checking the provided sequence file Detected sequence length: 289 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 289 Adjusted target solvent content: 0.60 Input MTZ file: 1vpy-3.6-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: 170 Cell parameters: 114.136 114.136 52.333 90.000 90.000 120.000 Input sequence file: 1vpy-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2312 target number of atoms Had to go as low as 0.85 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 Loops will be built when appropriate and at the last cycle Resolution range: 98.845 3.600 Wilson plot Bfac: 70.40 4625 reflections ( 99.74 % complete ) and 0 restraints for refining 2574 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3080 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2841 (Rfree = 0.000) for 2574 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.08 Search for helices and strands: 0 residues in 0 chains, 2621 seeds are put forward Round 1: 125 peptides, 19 chains. Longest chain 21 peptides. Score 0.406 Round 2: 154 peptides, 20 chains. Longest chain 32 peptides. Score 0.503 Round 3: 160 peptides, 21 chains. Longest chain 18 peptides. Score 0.508 Round 4: 164 peptides, 16 chains. Longest chain 26 peptides. Score 0.600 Round 5: 164 peptides, 17 chains. Longest chain 27 peptides. Score 0.585 Taking the results from Round 4 Chains 18, Residues 148, Estimated correctness of the model 14.7 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4751 restraints for refining 2096 atoms. 4143 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2450 (Rfree = 0.000) for 2096 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.2414 (Rfree = 0.000) for 2066 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 3: After refmac, R = 0.2452 (Rfree = 0.000) for 2063 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2244 (Rfree = 0.000) for 2058 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2334 (Rfree = 0.000) for 2053 atoms. Found 9 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 2.99 Search for helices and strands: 0 residues in 0 chains, 2153 seeds are put forward Round 1: 159 peptides, 22 chains. Longest chain 27 peptides. Score 0.487 Round 2: 164 peptides, 19 chains. Longest chain 30 peptides. Score 0.554 Round 3: 181 peptides, 23 chains. Longest chain 25 peptides. Score 0.549 Round 4: 177 peptides, 18 chains. Longest chain 34 peptides. Score 0.611 Round 5: 179 peptides, 21 chains. Longest chain 35 peptides. Score 0.573 Taking the results from Round 4 Chains 18, Residues 159, Estimated correctness of the model 18.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4579 restraints for refining 2063 atoms. 3961 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2692 (Rfree = 0.000) for 2063 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 7: After refmac, R = 0.2443 (Rfree = 0.000) for 2045 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 8: After refmac, R = 0.2224 (Rfree = 0.000) for 2035 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2290 (Rfree = 0.000) for 2020 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 10: After refmac, R = 0.2110 (Rfree = 0.000) for 2012 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.00 Search for helices and strands: 0 residues in 0 chains, 2096 seeds are put forward Round 1: 149 peptides, 19 chains. Longest chain 26 peptides. Score 0.501 Round 2: 172 peptides, 19 chains. Longest chain 27 peptides. Score 0.581 Round 3: 176 peptides, 20 chains. Longest chain 29 peptides. Score 0.578 Round 4: 162 peptides, 22 chains. Longest chain 18 peptides. Score 0.499 Round 5: 166 peptides, 19 chains. Longest chain 26 peptides. Score 0.561 Taking the results from Round 2 Chains 19, Residues 153, Estimated correctness of the model 7.1 % 1 chains (26 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4421 restraints for refining 2095 atoms. 3712 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2474 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 12: After refmac, R = 0.2371 (Rfree = 0.000) for 2078 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2185 (Rfree = 0.000) for 2072 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 14: After refmac, R = 0.1967 (Rfree = 0.000) for 2061 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 2056 atoms. Found 6 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.02 Search for helices and strands: 0 residues in 0 chains, 2138 seeds are put forward Round 1: 162 peptides, 23 chains. Longest chain 21 peptides. Score 0.482 Round 2: 165 peptides, 18 chains. Longest chain 22 peptides. Score 0.573 Round 3: 167 peptides, 18 chains. Longest chain 32 peptides. Score 0.579 Round 4: 156 peptides, 18 chains. Longest chain 25 peptides. Score 0.543 Round 5: 166 peptides, 18 chains. Longest chain 26 peptides. Score 0.576 Taking the results from Round 3 Chains 22, Residues 149, Estimated correctness of the model 6.3 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4361 restraints for refining 2095 atoms. 3606 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2368 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 17: After refmac, R = 0.2209 (Rfree = 0.000) for 2062 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2192 (Rfree = 0.000) for 2059 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2122 (Rfree = 0.000) for 2056 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 20: After refmac, R = 0.2047 (Rfree = 0.000) for 2051 atoms. Found 11 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 2132 seeds are put forward Round 1: 155 peptides, 24 chains. Longest chain 15 peptides. Score 0.438 Round 2: 151 peptides, 19 chains. Longest chain 27 peptides. Score 0.508 Round 3: 162 peptides, 21 chains. Longest chain 26 peptides. Score 0.515 Round 4: 164 peptides, 18 chains. Longest chain 30 peptides. Score 0.570 Round 5: 163 peptides, 19 chains. Longest chain 27 peptides. Score 0.551 Taking the results from Round 4 Chains 20, Residues 146, Estimated correctness of the model 2.6 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4654 restraints for refining 2096 atoms. 4051 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2397 (Rfree = 0.000) for 2096 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.2346 (Rfree = 0.000) for 2088 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2148 (Rfree = 0.000) for 2073 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.2253 (Rfree = 0.000) for 2066 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 25: After refmac, R = 0.2054 (Rfree = 0.000) for 2064 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 2150 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 12 peptides. Score 0.406 Round 2: 165 peptides, 20 chains. Longest chain 22 peptides. Score 0.542 Round 3: 169 peptides, 17 chains. Longest chain 21 peptides. Score 0.601 Round 4: 175 peptides, 19 chains. Longest chain 31 peptides. Score 0.590 Round 5: 166 peptides, 18 chains. Longest chain 29 peptides. Score 0.576 Taking the results from Round 3 Chains 17, Residues 152, Estimated correctness of the model 15.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4454 restraints for refining 2095 atoms. 3818 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2214 (Rfree = 0.000) for 2095 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 2093 atoms. Found 12 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2237 (Rfree = 0.000) for 2089 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.2234 (Rfree = 0.000) for 2088 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.2080 (Rfree = 0.000) for 2087 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.03 Search for helices and strands: 0 residues in 0 chains, 2152 seeds are put forward Round 1: 141 peptides, 19 chains. Longest chain 16 peptides. Score 0.471 Round 2: 167 peptides, 21 chains. Longest chain 34 peptides. Score 0.533 Round 3: 168 peptides, 20 chains. Longest chain 21 peptides. Score 0.552 Round 4: 167 peptides, 20 chains. Longest chain 25 peptides. Score 0.549 Round 5: 172 peptides, 19 chains. Longest chain 25 peptides. Score 0.581 Taking the results from Round 5 Chains 23, Residues 153, Estimated correctness of the model 7.1 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4253 restraints for refining 2096 atoms. 3521 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2576 (Rfree = 0.000) for 2096 atoms. Found 13 (13 requested) and removed 44 (6 requested) atoms. Cycle 32: After refmac, R = 0.2362 (Rfree = 0.000) for 2055 atoms. Found 9 (13 requested) and removed 15 (6 requested) atoms. Cycle 33: After refmac, R = 0.2331 (Rfree = 0.000) for 2040 atoms. Found 7 (13 requested) and removed 18 (6 requested) atoms. Cycle 34: After refmac, R = 0.2340 (Rfree = 0.000) for 2027 atoms. Found 11 (13 requested) and removed 18 (6 requested) atoms. Cycle 35: After refmac, R = 0.2245 (Rfree = 0.000) for 2012 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.00 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.325 Round 2: 141 peptides, 18 chains. Longest chain 16 peptides. Score 0.488 Round 3: 140 peptides, 17 chains. Longest chain 22 peptides. Score 0.502 Round 4: 135 peptides, 19 chains. Longest chain 15 peptides. Score 0.447 Round 5: 135 peptides, 16 chains. Longest chain 19 peptides. Score 0.501 Taking the results from Round 3 Chains 19, Residues 123, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4599 restraints for refining 2061 atoms. 4084 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2364 (Rfree = 0.000) for 2061 atoms. Found 11 (13 requested) and removed 23 (6 requested) atoms. Cycle 37: After refmac, R = 0.2593 (Rfree = 0.000) for 2041 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 38: After refmac, R = 0.2243 (Rfree = 0.000) for 2032 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.1928 (Rfree = 0.000) for 2027 atoms. Found 6 (13 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.1924 (Rfree = 0.000) for 2023 atoms. Found 5 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.04 Search for helices and strands: 0 residues in 0 chains, 2083 seeds are put forward Round 1: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.362 Round 2: 138 peptides, 21 chains. Longest chain 15 peptides. Score 0.423 Round 3: 152 peptides, 23 chains. Longest chain 13 peptides. Score 0.444 Round 4: 136 peptides, 20 chains. Longest chain 17 peptides. Score 0.433 Round 5: 136 peptides, 20 chains. Longest chain 14 peptides. Score 0.433 Taking the results from Round 3 Chains 23, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4625 reflections ( 99.74 % complete ) and 4575 restraints for refining 2056 atoms. 4082 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2374 (Rfree = 0.000) for 2056 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. *** WARNING *** Conditional restraints for refinement could not be generated Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 2059 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 43: After refmac, R = 0.2089 (Rfree = 0.000) for 2055 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.2131 (Rfree = 0.000) for 2054 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2233 (Rfree = 0.000) for 2053 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.08 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward Round 1: 139 peptides, 25 chains. Longest chain 16 peptides. Score 0.353 Round 2: 149 peptides, 24 chains. Longest chain 16 peptides. Score 0.414 Round 3: 163 peptides, 25 chains. Longest chain 11 peptides. Score 0.452 Round 4: 148 peptides, 21 chains. Longest chain 16 peptides. Score 0.463 Round 5: 149 peptides, 23 chains. Longest chain 15 peptides. Score 0.432 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 127, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vpy-3_warpNtrace.pdb as input Building loops using Loopy2018 21 chains (127 residues) following loop building 2 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4625 reflections ( 99.74 % complete ) and 4587 restraints for refining 2096 atoms. 4035 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2417 (Rfree = 0.000) for 2096 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2614 (Rfree = 0.000) for 2085 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2446 (Rfree = 0.000) for 2077 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2198 (Rfree = 0.000) for 2069 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:09:41 GMT 2018 Job finished. TimeTaking 46.65 Used memory is bytes: 172064