Sun 23 Dec 22:22:40 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 2p4g-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4g-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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/2p4g-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 ============================================================ Sun 23 Dec 22:22:49 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/2p4g-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4g-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 277 and 0 Target number of residues in the AU: 277 Target solvent content: 0.6590 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 270 Adjusted target solvent content: 0.67 Input MTZ file: 2p4g-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: 172 Cell parameters: 115.650 115.650 56.930 90.000 90.000 120.000 Input sequence file: 2p4g-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2160 target number of atoms Had to go as low as 1.10 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: 28.913 3.401 Wilson plot Bfac: 84.06 6090 reflections ( 99.72 % complete ) and 0 restraints for refining 2417 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3500 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2928 (Rfree = 0.000) for 2417 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 2.75 Search for helices and strands: 0 residues in 0 chains, 2465 seeds are put forward Round 1: 136 peptides, 23 chains. Longest chain 11 peptides. Score 0.362 Round 2: 160 peptides, 20 chains. Longest chain 16 peptides. Score 0.498 Round 3: 158 peptides, 19 chains. Longest chain 26 peptides. Score 0.507 Round 4: 172 peptides, 19 chains. Longest chain 26 peptides. Score 0.551 Round 5: 162 peptides, 20 chains. Longest chain 15 peptides. Score 0.505 Taking the results from Round 4 Chains 20, Residues 153, Estimated correctness of the model 11.8 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 4166 restraints for refining 1964 atoms. 3532 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2960 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 2: After refmac, R = 0.2864 (Rfree = 0.000) for 1962 atoms. Found 14 (14 requested) and removed 8 (7 requested) atoms. Cycle 3: After refmac, R = 0.2900 (Rfree = 0.000) for 1965 atoms. Found 10 (14 requested) and removed 11 (7 requested) atoms. Cycle 4: After refmac, R = 0.2835 (Rfree = 0.000) for 1962 atoms. Found 11 (14 requested) and removed 13 (7 requested) atoms. Cycle 5: After refmac, R = 0.2788 (Rfree = 0.000) for 1960 atoms. Found 5 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 2.76 Search for helices and strands: 0 residues in 0 chains, 2032 seeds are put forward Round 1: 164 peptides, 21 chains. Longest chain 13 peptides. Score 0.496 Round 2: 168 peptides, 22 chains. Longest chain 16 peptides. Score 0.494 Round 3: 173 peptides, 21 chains. Longest chain 17 peptides. Score 0.526 Round 4: 173 peptides, 18 chains. Longest chain 22 peptides. Score 0.569 Round 5: 177 peptides, 17 chains. Longest chain 26 peptides. Score 0.594 Taking the results from Round 5 Chains 19, Residues 160, Estimated correctness of the model 26.6 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 4193 restraints for refining 1964 atoms. 3528 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2984 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 7: After refmac, R = 0.2719 (Rfree = 0.000) for 1966 atoms. Found 9 (14 requested) and removed 9 (7 requested) atoms. Cycle 8: After refmac, R = 0.2604 (Rfree = 0.000) for 1963 atoms. Found 13 (14 requested) and removed 16 (7 requested) atoms. Cycle 9: After refmac, R = 0.2541 (Rfree = 0.000) for 1958 atoms. Found 10 (14 requested) and removed 15 (7 requested) atoms. Cycle 10: After refmac, R = 0.2462 (Rfree = 0.000) for 1951 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.48 2.75 Search for helices and strands: 0 residues in 0 chains, 2011 seeds are put forward Round 1: 161 peptides, 25 chains. Longest chain 13 peptides. Score 0.423 Round 2: 165 peptides, 20 chains. Longest chain 17 peptides. Score 0.515 Round 3: 166 peptides, 20 chains. Longest chain 25 peptides. Score 0.518 Round 4: 178 peptides, 22 chains. Longest chain 16 peptides. Score 0.527 Round 5: 176 peptides, 21 chains. Longest chain 18 peptides. Score 0.535 Taking the results from Round 5 Chains 21, Residues 155, Estimated correctness of the model 6.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 4238 restraints for refining 1963 atoms. 3639 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2660 (Rfree = 0.000) for 1963 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 12: After refmac, R = 0.2485 (Rfree = 0.000) for 1957 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 13: After refmac, R = 0.2355 (Rfree = 0.000) for 1946 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 14: After refmac, R = 0.2257 (Rfree = 0.000) for 1940 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. Cycle 15: After refmac, R = 0.2192 (Rfree = 0.000) for 1928 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.73 Search for helices and strands: 0 residues in 0 chains, 2001 seeds are put forward Round 1: 173 peptides, 25 chains. Longest chain 16 peptides. Score 0.465 Round 2: 177 peptides, 21 chains. Longest chain 31 peptides. Score 0.538 Round 3: 175 peptides, 19 chains. Longest chain 17 peptides. Score 0.561 Round 4: 168 peptides, 20 chains. Longest chain 24 peptides. Score 0.524 Round 5: 178 peptides, 20 chains. Longest chain 23 peptides. Score 0.555 Taking the results from Round 3 Chains 20, Residues 156, Estimated correctness of the model 15.4 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 4030 restraints for refining 1964 atoms. 3391 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2482 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 17: After refmac, R = 0.2351 (Rfree = 0.000) for 1966 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 18: After refmac, R = 0.2261 (Rfree = 0.000) for 1960 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 19: After refmac, R = 0.2222 (Rfree = 0.000) for 1956 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. Cycle 20: After refmac, R = 0.2215 (Rfree = 0.000) for 1948 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.76 Search for helices and strands: 0 residues in 0 chains, 2002 seeds are put forward Round 1: 165 peptides, 25 chains. Longest chain 15 peptides. Score 0.437 Round 2: 166 peptides, 22 chains. Longest chain 16 peptides. Score 0.488 Round 3: 170 peptides, 21 chains. Longest chain 25 peptides. Score 0.516 Round 4: 181 peptides, 20 chains. Longest chain 33 peptides. Score 0.565 Round 5: 169 peptides, 18 chains. Longest chain 26 peptides. Score 0.557 Taking the results from Round 4 Chains 22, Residues 161, Estimated correctness of the model 16.8 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 3846 restraints for refining 1964 atoms. 3128 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2588 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 10 (7 requested) atoms. Cycle 22: After refmac, R = 0.2393 (Rfree = 0.000) for 1961 atoms. Found 13 (14 requested) and removed 7 (7 requested) atoms. Cycle 23: After refmac, R = 0.2318 (Rfree = 0.000) for 1965 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Cycle 24: After refmac, R = 0.2286 (Rfree = 0.000) for 1961 atoms. Found 7 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2232 (Rfree = 0.000) for 1961 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 2.76 Search for helices and strands: 0 residues in 0 chains, 2013 seeds are put forward Round 1: 149 peptides, 26 chains. Longest chain 21 peptides. Score 0.361 Round 2: 167 peptides, 21 chains. Longest chain 22 peptides. Score 0.506 Round 3: 169 peptides, 22 chains. Longest chain 14 peptides. Score 0.498 Round 4: 175 peptides, 19 chains. Longest chain 28 peptides. Score 0.561 Round 5: 176 peptides, 19 chains. Longest chain 28 peptides. Score 0.564 Taking the results from Round 5 Chains 19, Residues 157, Estimated correctness of the model 16.4 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 3747 restraints for refining 1963 atoms. 3000 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2581 (Rfree = 0.000) for 1963 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2425 (Rfree = 0.000) for 1964 atoms. Found 11 (14 requested) and removed 7 (7 requested) atoms. Cycle 28: After refmac, R = 0.2328 (Rfree = 0.000) for 1966 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. Cycle 29: After refmac, R = 0.2281 (Rfree = 0.000) for 1964 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 30: After refmac, R = 0.2231 (Rfree = 0.000) for 1961 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 2.75 Search for helices and strands: 0 residues in 0 chains, 2022 seeds are put forward Round 1: 155 peptides, 27 chains. Longest chain 10 peptides. Score 0.368 Round 2: 151 peptides, 18 chains. Longest chain 28 peptides. Score 0.499 Round 3: 173 peptides, 24 chains. Longest chain 18 peptides. Score 0.481 Round 4: 174 peptides, 22 chains. Longest chain 16 peptides. Score 0.514 Round 5: 180 peptides, 20 chains. Longest chain 22 peptides. Score 0.562 Taking the results from Round 5 Chains 22, Residues 160, Estimated correctness of the model 15.7 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 3893 restraints for refining 1964 atoms. 3205 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2535 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Cycle 32: After refmac, R = 0.2333 (Rfree = 0.000) for 1964 atoms. Found 7 (14 requested) and removed 8 (7 requested) atoms. Cycle 33: After refmac, R = 0.2242 (Rfree = 0.000) for 1962 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 34: After refmac, R = 0.2150 (Rfree = 0.000) for 1960 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 35: After refmac, R = 0.2115 (Rfree = 0.000) for 1955 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 2.77 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward Round 1: 148 peptides, 26 chains. Longest chain 11 peptides. Score 0.357 Round 2: 159 peptides, 22 chains. Longest chain 14 peptides. Score 0.464 Round 3: 143 peptides, 16 chains. Longest chain 20 peptides. Score 0.504 Round 4: 154 peptides, 20 chains. Longest chain 20 peptides. Score 0.478 Round 5: 156 peptides, 19 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 3 Chains 16, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6090 reflections ( 99.72 % complete ) and 4387 restraints for refining 1964 atoms. 3895 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2433 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 37: After refmac, R = 0.2236 (Rfree = 0.000) for 1968 atoms. Found 4 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2165 (Rfree = 0.000) for 1962 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 39: After refmac, R = 0.2158 (Rfree = 0.000) for 1952 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 40: After refmac, R = 0.2116 (Rfree = 0.000) for 1946 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 2.77 Search for helices and strands: 0 residues in 0 chains, 2004 seeds are put forward Round 1: 135 peptides, 22 chains. Longest chain 17 peptides. Score 0.375 Round 2: 141 peptides, 20 chains. Longest chain 18 peptides. Score 0.432 Round 3: 135 peptides, 19 chains. Longest chain 17 peptides. Score 0.427 Round 4: 142 peptides, 17 chains. Longest chain 14 peptides. Score 0.485 Round 5: 148 peptides, 21 chains. Longest chain 19 peptides. Score 0.441 Taking the results from Round 4 Chains 17, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6090 reflections ( 99.72 % complete ) and 4423 restraints for refining 1964 atoms. 3940 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2240 (Rfree = 0.000) for 1964 atoms. Found 14 (14 requested) and removed 7 (7 requested) atoms. Cycle 42: After refmac, R = 0.2004 (Rfree = 0.000) for 1969 atoms. Found 6 (14 requested) and removed 8 (7 requested) atoms. Cycle 43: After refmac, R = 0.1972 (Rfree = 0.000) for 1959 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 44: After refmac, R = 0.1933 (Rfree = 0.000) for 1952 atoms. Found 2 (14 requested) and removed 7 (7 requested) atoms. Cycle 45: After refmac, R = 0.1945 (Rfree = 0.000) for 1946 atoms. Found 1 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 2.77 Search for helices and strands: 0 residues in 0 chains, 2019 seeds are put forward Round 1: 126 peptides, 22 chains. Longest chain 10 peptides. Score 0.339 Round 2: 130 peptides, 19 chains. Longest chain 11 peptides. Score 0.408 Round 3: 149 peptides, 20 chains. Longest chain 13 peptides. Score 0.461 Round 4: 149 peptides, 20 chains. Longest chain 19 peptides. Score 0.461 Round 5: 165 peptides, 20 chains. Longest chain 22 peptides. Score 0.515 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 145, 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 2p4g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6090 reflections ( 99.72 % complete ) and 4160 restraints for refining 1964 atoms. 3600 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2262 (Rfree = 0.000) for 1964 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2136 (Rfree = 0.000) for 1952 atoms. Found 0 (14 requested) and removed 4 (7 requested) atoms. Cycle 48: After refmac, R = 0.2018 (Rfree = 0.000) for 1945 atoms. Found 0 (14 requested) and removed 5 (7 requested) atoms. Cycle 49: After refmac, R = 0.1996 (Rfree = 0.000) for 1938 atoms. TimeTaking 46.6