Sun 23 Dec 22:22:43 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 2gjg-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gjg-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-2.2-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/2gjg-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-2.2-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 22:22:53 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/2gjg-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gjg-2.2-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 249 and 0 Target number of residues in the AU: 249 Target solvent content: 0.4641 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 248 Adjusted target solvent content: 0.47 Input MTZ file: 2gjg-2.2-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: 5 Cell parameters: 89.350 48.920 57.630 90.000 93.310 90.000 Input sequence file: 2gjg-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1984 target number of atoms Had to go as low as 0.50 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 1 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: 28.767 2.201 Wilson plot Bfac: 16.68 12240 reflections ( 95.90 % complete ) and 0 restraints for refining 2187 atoms. Observations/parameters ratio is 1.40 ------------------------------------------------------ Starting model: R = 0.3607 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3234 (Rfree = 0.000) for 2187 atoms. Found 44 (57 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 2.18 Round 1: 122 peptides, 25 chains. Longest chain 8 peptides. Score 0.321 Round 2: 136 peptides, 24 chains. Longest chain 14 peptides. Score 0.435 Round 3: 148 peptides, 22 chains. Longest chain 20 peptides. Score 0.549 Round 4: 162 peptides, 22 chains. Longest chain 27 peptides. Score 0.616 Round 5: 163 peptides, 22 chains. Longest chain 28 peptides. Score 0.620 Taking the results from Round 5 Chains 23, Residues 141, Estimated correctness of the model 83.6 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3561 restraints for refining 1894 atoms. 2900 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3634 (Rfree = 0.000) for 1894 atoms. Found 47 (49 requested) and removed 28 (24 requested) atoms. Cycle 2: After refmac, R = 0.3457 (Rfree = 0.000) for 1912 atoms. Found 35 (49 requested) and removed 24 (24 requested) atoms. Cycle 3: After refmac, R = 0.3339 (Rfree = 0.000) for 1918 atoms. Found 27 (50 requested) and removed 25 (25 requested) atoms. Cycle 4: After refmac, R = 0.3240 (Rfree = 0.000) for 1919 atoms. Found 29 (50 requested) and removed 19 (25 requested) atoms. Cycle 5: After refmac, R = 0.3227 (Rfree = 0.000) for 1927 atoms. Found 22 (50 requested) and removed 23 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.15 2.24 Round 1: 144 peptides, 21 chains. Longest chain 15 peptides. Score 0.551 Round 2: 154 peptides, 18 chains. Longest chain 24 peptides. Score 0.659 Round 3: 149 peptides, 16 chains. Longest chain 25 peptides. Score 0.676 Round 4: 150 peptides, 16 chains. Longest chain 25 peptides. Score 0.680 Round 5: 162 peptides, 16 chains. Longest chain 37 peptides. Score 0.724 Taking the results from Round 5 Chains 18, Residues 146, Estimated correctness of the model 90.9 % 2 chains (46 residues) have been docked in sequence Building loops using Loopy2018 18 chains (146 residues) following loop building 2 chains (46 residues) in sequence following loop building ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3315 restraints for refining 1894 atoms. 2564 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3496 (Rfree = 0.000) for 1894 atoms. Found 49 (49 requested) and removed 28 (24 requested) atoms. Cycle 7: After refmac, R = 0.3300 (Rfree = 0.000) for 1914 atoms. Found 40 (48 requested) and removed 24 (24 requested) atoms. Cycle 8: After refmac, R = 0.3162 (Rfree = 0.000) for 1928 atoms. Found 39 (48 requested) and removed 26 (25 requested) atoms. Cycle 9: After refmac, R = 0.3071 (Rfree = 0.000) for 1939 atoms. Found 39 (47 requested) and removed 19 (25 requested) atoms. Cycle 10: After refmac, R = 0.3010 (Rfree = 0.000) for 1955 atoms. Found 40 (48 requested) and removed 15 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 2.08 Round 1: 150 peptides, 18 chains. Longest chain 28 peptides. Score 0.642 Round 2: 153 peptides, 17 chains. Longest chain 30 peptides. Score 0.673 Round 3: 153 peptides, 17 chains. Longest chain 25 peptides. Score 0.673 Round 4: 162 peptides, 19 chains. Longest chain 25 peptides. Score 0.673 Round 5: 151 peptides, 19 chains. Longest chain 25 peptides. Score 0.626 Taking the results from Round 4 Chains 20, Residues 143, Estimated correctness of the model 87.6 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3438 restraints for refining 1930 atoms. 2747 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3250 (Rfree = 0.000) for 1930 atoms. Found 47 (47 requested) and removed 30 (25 requested) atoms. Cycle 12: After refmac, R = 0.3136 (Rfree = 0.000) for 1945 atoms. Found 42 (47 requested) and removed 25 (25 requested) atoms. Cycle 13: After refmac, R = 0.3043 (Rfree = 0.000) for 1961 atoms. Found 29 (48 requested) and removed 18 (25 requested) atoms. Cycle 14: After refmac, R = 0.3021 (Rfree = 0.000) for 1970 atoms. Found 47 (48 requested) and removed 10 (25 requested) atoms. Cycle 15: After refmac, R = 0.2924 (Rfree = 0.000) for 2007 atoms. Found 25 (49 requested) and removed 11 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.99 2.07 Round 1: 148 peptides, 20 chains. Longest chain 17 peptides. Score 0.592 Round 2: 157 peptides, 21 chains. Longest chain 22 peptides. Score 0.613 Round 3: 165 peptides, 22 chains. Longest chain 26 peptides. Score 0.629 Round 4: 154 peptides, 24 chains. Longest chain 14 peptides. Score 0.535 Round 5: 158 peptides, 21 chains. Longest chain 23 peptides. Score 0.618 Taking the results from Round 3 Chains 24, Residues 143, Estimated correctness of the model 84.3 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3495 restraints for refining 1953 atoms. 2895 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3150 (Rfree = 0.000) for 1953 atoms. Found 47 (47 requested) and removed 24 (25 requested) atoms. Cycle 17: After refmac, R = 0.2973 (Rfree = 0.000) for 1976 atoms. Found 34 (48 requested) and removed 10 (25 requested) atoms. Cycle 18: After refmac, R = 0.2894 (Rfree = 0.000) for 2000 atoms. Found 32 (49 requested) and removed 13 (26 requested) atoms. Cycle 19: After refmac, R = 0.2830 (Rfree = 0.000) for 2019 atoms. Found 40 (49 requested) and removed 12 (26 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2795 (Rfree = 0.000) for 2047 atoms. Found 29 (50 requested) and removed 12 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 2.07 Round 1: 148 peptides, 21 chains. Longest chain 18 peptides. Score 0.571 Round 2: 147 peptides, 19 chains. Longest chain 18 peptides. Score 0.608 Round 3: 142 peptides, 20 chains. Longest chain 15 peptides. Score 0.563 Round 4: 153 peptides, 19 chains. Longest chain 16 peptides. Score 0.635 Round 5: 155 peptides, 21 chains. Longest chain 16 peptides. Score 0.604 Taking the results from Round 4 Chains 19, Residues 134, Estimated correctness of the model 84.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3548 restraints for refining 1974 atoms. 2969 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3030 (Rfree = 0.000) for 1974 atoms. Found 48 (48 requested) and removed 26 (25 requested) atoms. Cycle 22: After refmac, R = 0.2938 (Rfree = 0.000) for 1994 atoms. Found 48 (48 requested) and removed 13 (25 requested) atoms. Cycle 23: After refmac, R = 0.2877 (Rfree = 0.000) for 2029 atoms. Found 28 (49 requested) and removed 11 (26 requested) atoms. Cycle 24: After refmac, R = 0.2796 (Rfree = 0.000) for 2045 atoms. Found 26 (50 requested) and removed 10 (26 requested) atoms. Cycle 25: After refmac, R = 0.2757 (Rfree = 0.000) for 2059 atoms. Found 25 (50 requested) and removed 15 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 2.07 Round 1: 140 peptides, 19 chains. Longest chain 15 peptides. Score 0.575 Round 2: 140 peptides, 18 chains. Longest chain 13 peptides. Score 0.597 Round 3: 146 peptides, 20 chains. Longest chain 13 peptides. Score 0.583 Round 4: 137 peptides, 17 chains. Longest chain 14 peptides. Score 0.604 Round 5: 139 peptides, 16 chains. Longest chain 19 peptides. Score 0.634 Taking the results from Round 5 Chains 18, Residues 123, Estimated correctness of the model 84.7 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3585 restraints for refining 2044 atoms. 2991 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3071 (Rfree = 0.000) for 2044 atoms. Found 50 (50 requested) and removed 31 (26 requested) atoms. Cycle 27: After refmac, R = 0.2966 (Rfree = 0.000) for 2063 atoms. Found 31 (50 requested) and removed 18 (26 requested) atoms. Cycle 28: After refmac, R = 0.2880 (Rfree = 0.000) for 2076 atoms. Found 35 (51 requested) and removed 14 (27 requested) atoms. Cycle 29: After refmac, R = 0.2813 (Rfree = 0.000) for 2097 atoms. Found 31 (51 requested) and removed 13 (27 requested) atoms. Cycle 30: After refmac, R = 0.2773 (Rfree = 0.000) for 2114 atoms. Found 27 (52 requested) and removed 10 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.96 2.04 Round 1: 119 peptides, 16 chains. Longest chain 16 peptides. Score 0.536 Round 2: 122 peptides, 14 chains. Longest chain 16 peptides. Score 0.598 Round 3: 127 peptides, 14 chains. Longest chain 18 peptides. Score 0.621 Round 4: 123 peptides, 13 chains. Longest chain 18 peptides. Score 0.624 Round 5: 134 peptides, 16 chains. Longest chain 18 peptides. Score 0.611 Taking the results from Round 4 Chains 15, Residues 110, Estimated correctness of the model 83.9 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3584 restraints for refining 2067 atoms. 3041 conditional restraints added. Observations/parameters ratio is 1.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2957 (Rfree = 0.000) for 2067 atoms. Found 50 (50 requested) and removed 28 (26 requested) atoms. Cycle 32: After refmac, R = 0.2838 (Rfree = 0.000) for 2088 atoms. Found 51 (51 requested) and removed 15 (27 requested) atoms. Cycle 33: After refmac, R = 0.2730 (Rfree = 0.000) for 2122 atoms. Found 23 (52 requested) and removed 7 (27 requested) atoms. Cycle 34: After refmac, R = 0.2659 (Rfree = 0.000) for 2134 atoms. Found 36 (52 requested) and removed 11 (27 requested) atoms. Cycle 35: After refmac, R = 0.2611 (Rfree = 0.000) for 2159 atoms. Found 26 (53 requested) and removed 14 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.98 2.06 Round 1: 124 peptides, 16 chains. Longest chain 18 peptides. Score 0.562 Round 2: 125 peptides, 17 chains. Longest chain 14 peptides. Score 0.544 Round 3: 123 peptides, 14 chains. Longest chain 17 peptides. Score 0.602 Round 4: 127 peptides, 15 chains. Longest chain 17 peptides. Score 0.599 Round 5: 118 peptides, 14 chains. Longest chain 17 peptides. Score 0.578 Taking the results from Round 3 Chains 14, Residues 109, Estimated correctness of the model 82.2 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3759 restraints for refining 2090 atoms. 3262 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2857 (Rfree = 0.000) for 2090 atoms. Found 51 (51 requested) and removed 28 (27 requested) atoms. Cycle 37: After refmac, R = 0.2772 (Rfree = 0.000) for 2113 atoms. Found 42 (52 requested) and removed 6 (27 requested) atoms. Cycle 38: After refmac, R = 0.2679 (Rfree = 0.000) for 2148 atoms. Found 29 (52 requested) and removed 13 (27 requested) atoms. Cycle 39: After refmac, R = 0.2620 (Rfree = 0.000) for 2162 atoms. Found 28 (53 requested) and removed 15 (28 requested) atoms. Cycle 40: After refmac, R = 0.2562 (Rfree = 0.000) for 2175 atoms. Found 20 (53 requested) and removed 15 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 2.06 Round 1: 107 peptides, 15 chains. Longest chain 16 peptides. Score 0.494 Round 2: 116 peptides, 14 chains. Longest chain 13 peptides. Score 0.568 Round 3: 118 peptides, 15 chains. Longest chain 15 peptides. Score 0.554 Round 4: 123 peptides, 14 chains. Longest chain 17 peptides. Score 0.602 Round 5: 117 peptides, 14 chains. Longest chain 15 peptides. Score 0.573 Taking the results from Round 4 Chains 14, Residues 109, Estimated correctness of the model 82.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12240 reflections ( 95.90 % complete ) and 3973 restraints for refining 2092 atoms. 3551 conditional restraints added. Observations/parameters ratio is 1.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2748 (Rfree = 0.000) for 2092 atoms. Found 51 (51 requested) and removed 5 (27 requested) atoms. Cycle 42: After refmac, R = 0.2639 (Rfree = 0.000) for 2138 atoms. Found 44 (52 requested) and removed 9 (27 requested) atoms. Cycle 43: After refmac, R = 0.2601 (Rfree = 0.000) for 2173 atoms. Found 30 (53 requested) and removed 7 (28 requested) atoms. Cycle 44: After refmac, R = 0.2545 (Rfree = 0.000) for 2195 atoms. Found 33 (54 requested) and removed 12 (28 requested) atoms. Cycle 45: After refmac, R = 0.2513 (Rfree = 0.000) for 2214 atoms. Found 24 (54 requested) and removed 9 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 2.10 Round 1: 118 peptides, 18 chains. Longest chain 15 peptides. Score 0.481 Round 2: 118 peptides, 15 chains. Longest chain 16 peptides. Score 0.554 Round 3: 124 peptides, 15 chains. Longest chain 16 peptides. Score 0.585 Round 4: 127 peptides, 15 chains. Longest chain 15 peptides. Score 0.599 Round 5: 124 peptides, 15 chains. Longest chain 17 peptides. Score 0.585 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 112, Estimated correctness of the model 81.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2gjg-2_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12240 reflections ( 95.90 % complete ) and 3954 restraints for refining 2129 atoms. 3521 conditional restraints added. Observations/parameters ratio is 1.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2747 (Rfree = 0.000) for 2129 atoms. Found 0 (52 requested) and removed 6 (27 requested) atoms. Cycle 47: After refmac, R = 0.2657 (Rfree = 0.000) for 2122 atoms. Found 0 (52 requested) and removed 3 (27 requested) atoms. Cycle 48: After refmac, R = 0.2601 (Rfree = 0.000) for 2119 atoms. Found 0 (52 requested) and removed 3 (27 requested) atoms. Cycle 49: After refmac, R = 0.2620 (Rfree = 0.000) for 2116 atoms. TimeTaking 32.88